| Title: | Make Complex Heatmaps |
|---|---|
| Description: | Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics. |
| Authors: | Zuguang Gu [aut, cre] |
| Maintainer: | Zuguang Gu <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 2.23.0 |
| Built: | 2024-10-30 05:19:43 UTC |
| Source: | https://github.com/bioc/ComplexHeatmap |
Make complex heatmaps
This package aims to provide a simple and flexible way to arrange multiple heatmaps as well as flexible annotation graphics.
The package is implemented in an object-oriented way. The heatmap lists are abstracted into several classes.
Heatmap-class: a single heatmap containing heatmap body, row/column names, titles, dendrograms and annotations.
HeatmapList-class: a list of heatmaps and annotations.
HeatmapAnnotation-class: a list of row/column annotations.
There are also several internal classes:
SingleAnnotation-class: a single row annotation or column annotation.
ColorMapping-class: mapping from values to colors.
AnnotationFunction-class: construct an annotation function which allows subsetting.
Following two high-level functions take use of functionality of complex heatmaps:
oncoPrint: oncoPrint plot which visualize genomic alterations in a set of genes.
densityHeatmap: use heatmaps to visualize density distributions.
The complete reference of ComplexHeatmap package is available at http://jokergoo.github.io/ComplexHeatmap-reference/book.
# There is no example NULL# There is no example NULL
Subset an AnnotationFunction Object
## S3 method for class 'AnnotationFunction' x[i]## S3 method for class 'AnnotationFunction' x[i]
x |
An |
i |
A vector of indices. |
One good thing for designing the AnnotationFunction-class is it can be subsetted,
and this is the base for the splitting of the annotations.
anno = anno_simple(1:10) anno[1:5] draw(anno[1:5], test = "subset of column annotation")anno = anno_simple(1:10) anno[1:5] draw(anno[1:5], test = "subset of column annotation")
Subset the Combination Matrix
## S3 method for class 'comb_mat' x[i, j, drop = FALSE]## S3 method for class 'comb_mat' x[i, j, drop = FALSE]
x |
A combination matrix returned by |
i |
Indices on rows. |
j |
Indices on columns. |
drop |
It is always reset to |
If sets are on rows of the combination matrix, the row indices correspond to sets and column indices correspond to combination sets, and if sets are on columns of the combination matrix, rows correspond to the combination sets.
If the index is one-dimension, e.g. x[i], the index always corresponds to the combination sets.
You should not subset by the sets. It will give you wrong combination set size. The subsetting on sets are only used internally.
This subsetting method is mainly for subsetting combination sets, i.e., users
can first use comb_size to get the size of each combination set, and filter them
by the size.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) m2 = m[, comb_size(m) >= 3] comb_size(m2) m[comb_size(m) >= 3]set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) m2 = m[, comb_size(m) >= 3] comb_size(m2) m[comb_size(m) >= 3]
Subset method of gridtext class
## S3 method for class 'gridtext' x[index]## S3 method for class 'gridtext' x[index]
x |
A vector of labels generated by |
index |
Index |
Internally used.
# There is no example NULL# There is no example NULL
Subset a Heatmap
## S3 method for class 'Heatmap' x[i, j]## S3 method for class 'Heatmap' x[i, j]
x |
A |
i |
Row indices. |
j |
Column indices. |
This functionality is quite experimental. It should be applied before the layout is initialized.
m = matrix(rnorm(100), nrow = 10) rownames(m) = letters[1:10] colnames(m) = LETTERS[1:10] ht = Heatmap(m) ht[1:5, ] ht[1:5] ht[, 1:5] ht[1:5, 1:5]m = matrix(rnorm(100), nrow = 10) rownames(m) = letters[1:10] colnames(m) = LETTERS[1:10] ht = Heatmap(m) ht[1:5, ] ht[1:5] ht[, 1:5] ht[1:5, 1:5]
Subset the HeatmapAnnotation object
## S3 method for class 'HeatmapAnnotation' x[i, j]## S3 method for class 'HeatmapAnnotation' x[i, j]
x |
A |
i |
Index of observations. |
j |
Index of annotations. |
ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1), sth = cbind(1:10, 10:1)) ha[1:5, ] ha[, c("foo", "bar")] ha[, 1:2] ha[1:5, c("foo", "sth")]ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1), sth = cbind(1:10, 10:1)) ha[1:5, ] ha[, c("foo", "bar")] ha[, 1:2] ha[1:5, c("foo", "sth")]
Subset a HeatmapList object
## S3 method for class 'HeatmapList' x[i, j]## S3 method for class 'HeatmapList' x[i, j]
x |
A |
i |
row indices |
j |
column indices |
If the heatmap list is horizontal, i is the row indices and j corresponds to heatmap names and single annotation names.
and if the heatlist is vertical, i corresponds to heatmap/annotation names and j is the column indices.
ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") + rowAnnotation(foo = 1:10, bar = anno_points(10:1)) + Heatmap(matrix(runif(100), 10), name = "runif") summary(ht_list[1:5, ]) summary(ht_list[1:5, 1]) summary(ht_list[1:5, "rnorm"]) summary(ht_list[1:5, c("rnorm", "foo")]) ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v% columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v% Heatmap(matrix(runif(100), 10), name = "runif") summary(ht_list[, 1:5]) summary(ht_list[1, 1:5]) summary(ht_list["rnorm", 1:5]) summary(ht_list[c("rnorm", "foo"), 1:5])ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") + rowAnnotation(foo = 1:10, bar = anno_points(10:1)) + Heatmap(matrix(runif(100), 10), name = "runif") summary(ht_list[1:5, ]) summary(ht_list[1:5, 1]) summary(ht_list[1:5, "rnorm"]) summary(ht_list[1:5, c("rnorm", "foo")]) ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v% columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v% Heatmap(matrix(runif(100), 10), name = "runif") summary(ht_list[, 1:5]) summary(ht_list[1, 1:5]) summary(ht_list["rnorm", 1:5]) summary(ht_list[c("rnorm", "foo"), 1:5])
Subset an SingleAnnotation Object
## S3 method for class 'SingleAnnotation' x[i]## S3 method for class 'SingleAnnotation' x[i]
x |
An |
i |
A vector of indices. |
The SingleAnnotation class object is subsettable only if the containing AnnotationFunction-class
object is subsettable. All the anno_* functions are subsettable, so if the SingleAnnotation object
is constructed by one of these functions, it is also subsettable.
ha = SingleAnnotation(value = 1:10) ha[1:5] draw(ha[1:5], test = "ha[1:5]")ha = SingleAnnotation(value = 1:10) ha[1:5] draw(ha[1:5], test = "ha[1:5]")
Vertically Add Heatmaps or Annotations to a Heatmap List
x %v% yx %v% y
x |
A |
y |
A |
It is only a helper function. It actually calls
add_heatmap,Heatmap-method, add_heatmap,HeatmapList-method or
add_heatmap,HeatmapAnnotation-method depending on the class of the input
objects.
The HeatmapAnnotation-class object to be added should only be column
annotations.
x and y can also be NULL.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
+.AdditiveUnit operator is used for horizontal heatmap list.
# There is no example NULL# There is no example NULL
Horizontally Add Heatmaps or Annotations to a Heatmap List
## S3 method for class 'AdditiveUnit' x + y## S3 method for class 'AdditiveUnit' x + y
x |
A |
y |
A |
It is only a helper function. It actually calls
add_heatmap,Heatmap-method, add_heatmap,HeatmapList-method or
add_heatmap,HeatmapAnnotation-method depending on the class of the input
objects.
The HeatmapAnnotation-class object to be added should only be row
annotations. Column annotations should be added to the heatmap list by
%v%.
x and y can also be NULL.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
%v% operator is used for vertical heatmap list.
# There is no example NULL# There is no example NULL
Method dispatch page for add_heatmap.
add_heatmap can be dispatched on following classes:
add_heatmap,HeatmapAnnotation-method, HeatmapAnnotation-class class method
add_heatmap,Heatmap-method, Heatmap-class class method
add_heatmap,HeatmapList-method, HeatmapList-class class method
# no example NULL# no example NULL
Add Heatmap to the Heatmap List
## S4 method for signature 'Heatmap' add_heatmap(object, x, direction = c("horizontal", "vertical"))## S4 method for signature 'Heatmap' add_heatmap(object, x, direction = c("horizontal", "vertical"))
object |
A |
x |
a |
direction |
Whether the heatmap is added horizontal or vertically? |
Normally we directly use + for horizontal concatenation and %v% for vertical concatenation.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Add Annotations or Heatmaps as a Heatmap List
## S4 method for signature 'HeatmapAnnotation' add_heatmap(object, x, direction = c("horizontal", "vertical"))## S4 method for signature 'HeatmapAnnotation' add_heatmap(object, x, direction = c("horizontal", "vertical"))
object |
A |
x |
A |
direction |
Whether it is horizontal list or a vertical list? |
Normally we directly use + for horizontal concatenation and %v% for vertical concatenation.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Add heatmaps and row annotations to the heatmap list
## S4 method for signature 'HeatmapList' add_heatmap(object, x, direction = c("horizontal", "vertical"))## S4 method for signature 'HeatmapList' add_heatmap(object, x, direction = c("horizontal", "vertical"))
object |
a |
x |
a |
direction |
direction of the concatenation. |
There is a shortcut function +.AdditiveUnit.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Constructor Method for AdditiveUnit Class
AdditiveUnit(...)AdditiveUnit(...)
... |
Black hole arguments. |
This method is not used in the package.
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Class for Concatenating Heatmaps and Annotations
This class is a super class for Heatmap-class, HeatmapList-class and
HeatmapAnnotation-class classes. It is only designed for + generic
method and the %v%v method so that above three classes can be appended to each other.
# There is no example NULL# There is no example NULL
Adjust the Positions of nodes/leaves in the Dendrogram
adjust_dend_by_x(dend, leaf_pos = 1:nobs(dend)-0.5)adjust_dend_by_x(dend, leaf_pos = 1:nobs(dend)-0.5)
dend |
A |
leaf_pos |
A vector of positions of leaves. The value can also be a |
The positions of nodes stored as x attribute are recalculated based on the new positions of leaves.
By default, the position of leaves are at 0.5, 1.5, ..., n-0.5.
m = matrix(rnorm(100), 10) dend = as.dendrogram(hclust(dist(m))) dend = adjust_dend_by_x(dend, sort(runif(10))) str(dend) dend = adjust_dend_by_x(dend, unit(1:10, "cm")) str(dend)m = matrix(rnorm(100), 10) dend = as.dendrogram(hclust(dist(m))) dend = adjust_dend_by_x(dend, sort(runif(10))) str(dend) dend = adjust_dend_by_x(dend, unit(1:10, "cm")) str(dend)
Adjust Heatmap List
## S4 method for signature 'HeatmapList' adjust_heatmap_list(object)## S4 method for signature 'HeatmapList' adjust_heatmap_list(object)
object |
A |
This function adjusts settings in all other heatmaps according to the main heatmap. It also adjust the size of heatmap annotations to make them aligned nicely.
This function is only for internal use.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Automatically generate alter_fun
alter_graphic(graphic = c("rect", "point"), width = 1, height = 1, horiz_margin = unit(1, "pt"), vertical_margin = unit(1, "pt"), fill = "red", col = NA, pch = 16, ...)alter_graphic(graphic = c("rect", "point"), width = 1, height = 1, horiz_margin = unit(1, "pt"), vertical_margin = unit(1, "pt"), fill = "red", col = NA, pch = 16, ...)
graphic |
Graphic to draw. |
width |
Relative width of the rectangle. |
height |
Relative height of the rectangle. |
horiz_margin |
Horizontal margin. E.g. if you want 1mm margin on top and 1mm margin at bottom of the rectangle, set this value to |
vertical_margin |
Vertical margin. |
fill |
Filled color. |
col |
Border color. |
pch |
Pch for points |
... |
Pass to |
This function aims to simplify the definition of functions in alter_fun. Now it only
supports rectangles and points.
mat = read.table(textConnection( "s1,s2,s3 g1,snv;indel,snv,indel g2,,snv;indel,snv g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE) mat = as.matrix(mat) col = c(snv = "red", indel = "blue") oncoPrint(mat, alter_fun = list( snv = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["snv"]), indel = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["indel"]) ), col = col)mat = read.table(textConnection( "s1,s2,s3 g1,snv;indel,snv,indel g2,,snv;indel,snv g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE) mat = as.matrix(mat) col = c(snv = "red", indel = "blue") oncoPrint(mat, alter_fun = list( snv = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["snv"]), indel = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["indel"]) ), col = col)
Barplot Annotation
anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, beside = FALSE, attach = FALSE, gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), add_numbers = FALSE, numbers_gp = gpar(fontsize = 8), numbers_rot = ifelse(which == "column", 45, 0), numbers_offset = unit(2, "mm"), width = NULL, height = NULL, ...)anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, beside = FALSE, attach = FALSE, gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), add_numbers = FALSE, numbers_gp = gpar(fontsize = 8), numbers_rot = ifelse(which == "column", 45, 0), numbers_offset = unit(2, "mm"), width = NULL, height = NULL, ...)
x |
The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. If |
baseline |
baseline of bars. The value should be "min" or "max", or a numeric value. It is enforced to be zero for stacked barplots. |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
bar_width |
Relative width of the bars. The value should be smaller than one. |
beside |
When |
attach |
When |
gp |
Graphic parameters for bars. The length of each graphic parameter can be 1, length of |
ylim |
Data ranges. By default it is |
extend |
The extension to both side of |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
add_numbers |
Whether to add numbers to the bars. It only works when |
numbers_gp |
Graphics parameters for the numbers. |
numbers_rot |
Rotation of numbers. |
numbers_offset |
Offset to the default positions (1mm away the top of the bars). |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
... |
Other arguments. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#barplot_annotation
anno = anno_barplot(1:10) draw(anno, test = "a vector") m = matrix(runif(4*10), nc = 4) m = t(apply(m, 1, function(x) x/sum(x))) anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm")) draw(anno, test = "proportion matrix")anno = anno_barplot(1:10) draw(anno, test = "a vector") m = matrix(runif(4*10), nc = 4) m = t(apply(m, 1, function(x) x/sum(x))) anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm")) draw(anno, test = "proportion matrix")
Block annotation
anno_block(align_to = NULL, gp = gpar(), labels = NULL, labels_gp = gpar(), labels_rot = ifelse(which == "row", 90, 0), labels_offset = unit(0.5, "npc"), labels_just = "center", which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE, panel_fun = NULL)anno_block(align_to = NULL, gp = gpar(), labels = NULL, labels_gp = gpar(), labels_rot = ifelse(which == "row", 90, 0), labels_offset = unit(0.5, "npc"), labels_just = "center", which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE, panel_fun = NULL)
align_to |
If you don't want to create block annotation for all slices, you can specify a list of indices that cover continuously adjacent rows or columns. |
gp |
Graphic parameters. |
labels |
Labels put on blocks. |
labels_gp |
Graphic parameters for labels. |
labels_rot |
Rotation for labels. |
labels_offset |
Positions of the labels. It controls offset on y-directions for column annotation and on x-directoin for row annotation. |
labels_just |
Jusification of the labels. |
which |
Is it a row annotation or a column annotation? |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
show_name |
Whether show annotatio name. |
panel_fun |
A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the current slice and 2. a vector of levels from the split variable that correspond to current slice. When |
The block annotation is used for representing slices. The length of all arguments should be 1 or the number of slices.
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation
Heatmap(matrix(rnorm(100), 10), top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4), labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))), column_km = 3, left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4), labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))), row_km = 3) # ============= set the panel_fun argument ============== col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange") Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block( panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90, gp = gpar(col = col[levels[1]])) } )) labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B") Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block(panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90, gp = gpar(col = col[levels[1]])) })) Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block( panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) txt = paste(levels, collapse = ",") txt = paste0(txt, "\n", length(index), " rows") grid.text(txt, 0.5, 0.5, rot = 0, gp = gpar(col = col[levels[1]])) }, width = unit(3, "cm") )) # =========== set align_to ################ col = c("foo" = "red", "bar" = "blue") Heatmap(matrix(rnorm(100), 10), cluster_rows = FALSE) + rowAnnotation(foo = anno_block( align_to = list(foo = 1:4, bar = 6:10), panel_fun = function(index, nm) { grid.rect(gp = gpar(fill = col[nm])) grid.text(nm, 0.5, 0.5) }, width = unit(2, "cm")) )Heatmap(matrix(rnorm(100), 10), top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4), labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))), column_km = 3, left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4), labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))), row_km = 3) # ============= set the panel_fun argument ============== col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange") Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block( panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90, gp = gpar(col = col[levels[1]])) } )) labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B") Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block(panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90, gp = gpar(col = col[levels[1]])) })) Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + rowAnnotation(foo = anno_block( panel_fun = function(index, levels) { grid.rect(gp = gpar(fill = col[levels[2]], col = "black")) txt = paste(levels, collapse = ",") txt = paste0(txt, "\n", length(index), " rows") grid.text(txt, 0.5, 0.5, rot = 0, gp = gpar(col = col[levels[1]])) }, width = unit(3, "cm") )) # =========== set align_to ################ col = c("foo" = "red", "bar" = "blue") Heatmap(matrix(rnorm(100), 10), cluster_rows = FALSE) + rowAnnotation(foo = anno_block( align_to = list(foo = 1:4, bar = 6:10), panel_fun = function(index, nm) { grid.rect(gp = gpar(fill = col[nm])) grid.text(nm, 0.5, 0.5) }, width = unit(2, "cm")) )
Boxplot Annotation
anno_boxplot(x, which = c("column", "row"), border = TRUE, gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, add_points = FALSE, pch = 16, size = unit(4, "pt"), pt_gp = gpar(), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL, ...)anno_boxplot(x, which = c("column", "row"), border = TRUE, gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, add_points = FALSE, pch = 16, size = unit(4, "pt"), pt_gp = gpar(), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL, ...)
x |
A matrix or a list. If |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations. |
ylim |
Data ranges. |
extend |
The extension to both side of |
outline |
Whether draw outline of boxplots? |
box_width |
Relative width of boxes. The value should be smaller than one. |
add_points |
Whether add points on top of the boxes? |
pch |
Point style. |
size |
Point size. |
pt_gp |
Graphics parameters for points. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
... |
Other arguments. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#box-annotation
set.seed(123) m = matrix(rnorm(100), 10) anno = anno_boxplot(m, height = unit(4, "cm")) draw(anno, test = "anno_boxplot") anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10)) draw(anno, test = "anno_boxplot with gp")set.seed(123) m = matrix(rnorm(100), 10) anno = anno_boxplot(m, height = unit(4, "cm")) draw(anno, test = "anno_boxplot") anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10)) draw(anno, test = "anno_boxplot with gp")
Customized annotation
anno_customize(x, graphics = list(), which = c("column", "row"), border = TRUE, width = NULL, height = NULL, verbose = TRUE)anno_customize(x, graphics = list(), which = c("column", "row"), border = TRUE, width = NULL, height = NULL, verbose = TRUE)
x |
A categorical variable. |
graphics |
A list of functions that define graphics for each level in |
which |
Is it a row annotation or a column annotation? |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
border |
Whether to draw border. |
verbose |
Whether to print messages. |
Functions in graphics define simple graphics drawn in each annotation cell. The function takes four arguments:
Center of the annotation cell.
Width and height of the annotation cell.
An annotation function which can be used in HeatmapAnnotation.
x = sort(sample(letters[1:3], 10, replace = TRUE)) graphics = list( "a" = function(x, y, w, h) grid.points(x, y, pch = 16), "b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")), "c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2)) ) anno = anno_customize(x, graphics = graphics) m = matrix(rnorm(100), 10) Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno)) # Add legends for `foo` ht = Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno)) lgd = Legend(title = "foo", at = names(graphics), graphics = graphics) draw(ht, annotation_legend_list = list(lgd))x = sort(sample(letters[1:3], 10, replace = TRUE)) graphics = list( "a" = function(x, y, w, h) grid.points(x, y, pch = 16), "b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")), "c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2)) ) anno = anno_customize(x, graphics = graphics) m = matrix(rnorm(100), 10) Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno)) # Add legends for `foo` ht = Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno)) lgd = Legend(title = "foo", at = names(graphics), graphics = graphics) draw(ht, annotation_legend_list = list(lgd))
Density Annotation
anno_density(x, which = c("column", "row"), type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL, heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)anno_density(x, which = c("column", "row"), type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL, heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)
x |
A matrix or a list. If |
which |
Whether it is a column annotation or a row annotation? |
type |
Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot and "heatmap" for heatmap visualization of density distribution. |
xlim |
Range on x-axis. |
max_density |
Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations and you want to compare between them, you should manually set this argument to make density distributions are in a same scale. |
heatmap_colors |
A vector of colors for interpolating density values. |
joyplot_scale |
Relative height of density distribution. A value higher than 1 increases the height of the density distribution and the plot will represented as so-called "joyplot". |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#density-annotation
m = matrix(rnorm(100), 10) anno = anno_density(m, which = "row") draw(anno, test = "normal density") anno = anno_density(m, which = "row", type = "violin") draw(anno, test = "violin") anno = anno_density(m, which = "row", type = "heatmap") draw(anno, test = "heatmap") anno = anno_density(m, which = "row", type = "heatmap", heatmap_colors = c("white", "orange")) draw(anno, test = "heatmap, colors")m = matrix(rnorm(100), 10) anno = anno_density(m, which = "row") draw(anno, test = "normal density") anno = anno_density(m, which = "row", type = "violin") draw(anno, test = "violin") anno = anno_density(m, which = "row", type = "heatmap") draw(anno, test = "heatmap") anno = anno_density(m, which = "row", type = "heatmap", heatmap_colors = c("white", "orange")) draw(anno, test = "heatmap, colors")
Empty Annotation
anno_empty(which = c("column", "row"), border = TRUE, zoom = FALSE, width = NULL, height = NULL, show_name = FALSE)anno_empty(which = c("column", "row"), border = TRUE, zoom = FALSE, width = NULL, height = NULL, show_name = FALSE)
which |
Whether it is a column annotation or a row annotation? |
border |
Whether draw borders of the annotation region? |
zoom |
If it is true and when the heatmap is split, the empty annotation slices will have equal height or width, and you can see the correspondance between the annotation slices and the original heatmap slices. |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
show_name |
Whether to show annotation name. |
It creates an empty annotation and holds space, later users can add graphics
by decorate_annotation. This function is useful when users have difficulty to
implement AnnotationFunction object.
In following example, an empty annotation is first created and later points are added:
m = matrix(rnorm(100), 10)
ht = Heatmap(m, top_annotation = HeatmapAnnotation(pt = anno_empty()))
ht = draw(ht)
co = column_order(ht)[[1]]
pt_value = 1:10
decorate_annotation("pt", {
pushViewport(viewport(xscale = c(0.5, ncol(mat)+0.5), yscale = range(pt_value)))
grid.points(seq_len(ncol(mat)), pt_value[co], pch = 16, default.units = "native")
grid.yaxis()
popViewport()
})
And it is similar as using anno_points:
Heatmap(m, top_annotation = HeatmapAnnotation(pt = anno_points(pt_value)))
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#empty-annotation
anno = anno_empty() draw(anno, test = "anno_empty") anno = anno_empty(border = FALSE) draw(anno, test = "anno_empty without border")anno = anno_empty() draw(anno, test = "anno_empty") anno = anno_empty(border = FALSE) draw(anno, test = "anno_empty without border")
Histogram Annotation
anno_histogram(x, which = c("column", "row"), n_breaks = 11, border = FALSE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)anno_histogram(x, which = c("column", "row"), n_breaks = 11, border = FALSE, gp = gpar(fill = "#CCCCCC"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)
x |
A matrix or a list. If |
which |
Whether it is a column annotation or a row annotation? |
n_breaks |
Number of breaks for calculating histogram. |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
An annotation function which can be used in HeatmapAnnotation.
m = matrix(rnorm(1000), nc = 10) anno = anno_histogram(t(m), which = "row") draw(anno, test = "row histogram") anno = anno_histogram(t(m), which = "row", gp = gpar(fill = 1:10)) draw(anno, test = "row histogram with color") anno = anno_histogram(t(m), which = "row", n_breaks = 20) draw(anno, test = "row histogram with color")m = matrix(rnorm(1000), nc = 10) anno = anno_histogram(t(m), which = "row") draw(anno, test = "row histogram") anno = anno_histogram(t(m), which = "row", gp = gpar(fill = 1:10)) draw(anno, test = "row histogram with color") anno = anno_histogram(t(m), which = "row", n_breaks = 20) draw(anno, test = "row histogram with color")
Horizon chart Annotation
anno_horizon(x, which = c("column", "row"), gp = gpar(pos_fill = "#D73027", neg_fill = "#313695"), n_slice = 4, slice_size = NULL, negative_from_top = FALSE, normalize = TRUE, gap = unit(0, "mm"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)anno_horizon(x, which = c("column", "row"), gp = gpar(pos_fill = "#D73027", neg_fill = "#313695"), n_slice = 4, slice_size = NULL, negative_from_top = FALSE, normalize = TRUE, gap = unit(0, "mm"), axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)
x |
A matrix or a list. If |
which |
Whether it is a column annotation or a row annotation? |
gp |
Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations. There are two unstandard parameters specificly for horizon chart: |
n_slice |
Number of slices on y-axis. |
slice_size |
Height of the slice. If the value is not |
negative_from_top |
Whether the areas for negative values start from the top or the bottom of the plotting region? |
normalize |
Whether normalize |
gap |
Gap size of neighbouring horizon chart. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
Horizon chart as row annotation is only supported.
An annotation function which can be used in HeatmapAnnotation.
lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1) anno = anno_horizon(lt, which = "row") draw(anno, test = "horizon chart") anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = "orange", neg_fill = "darkgreen")) draw(anno, test = "horizon chart, col") anno = anno_horizon(lt, which = "row", negative_from_top = TRUE) draw(anno, test = "horizon chart + negative_from_top") anno = anno_horizon(lt, which = "row", gap = unit(1, "mm")) draw(anno, test = "horizon chart + gap") anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = rep(c("orange", "red"), each = 10), neg_fill = rep(c("darkgreen", "blue"), each = 10))) draw(anno, test = "horizon chart, col")lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1) anno = anno_horizon(lt, which = "row") draw(anno, test = "horizon chart") anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = "orange", neg_fill = "darkgreen")) draw(anno, test = "horizon chart, col") anno = anno_horizon(lt, which = "row", negative_from_top = TRUE) draw(anno, test = "horizon chart + negative_from_top") anno = anno_horizon(lt, which = "row", gap = unit(1, "mm")) draw(anno, test = "horizon chart + gap") anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = rep(c("orange", "red"), each = 10), neg_fill = rep(c("darkgreen", "blue"), each = 10))) draw(anno, test = "horizon chart, col")
Image Annotation
anno_image(image, which = c("column", "row"), border = TRUE, gp = gpar(fill = NA, col = NA), space = unit(1, "mm"), width = NULL, height = NULL)anno_image(image, which = c("column", "row"), border = TRUE, gp = gpar(fill = NA, col = NA), space = unit(1, "mm"), width = NULL, height = NULL)
image |
A vector of file paths of images. The format of the image is inferred from the suffix name of the image file. NA values or empty strings in the vector means no image to drawn. |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for annotation grids. If the image has transparent background, the |
space |
The space around the image to the annotation grid borders. The value should be a |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
This function supports image formats in png, svg, pdf, eps, jpeg/jpg, tiff.
png, jpeg/jpg and tiff images are imported by readPNG, readJPEG and
readTIFF, and drawn by grid.raster. svg images are firstly reformatted by rsvg::rsvg_svg
and then imported by readPicture and drawn by grid.picture. pdf and eps
images are imported by PostScriptTrace and readPicture, later drawn by grid.picture.
Different image formats can be mixed in the image vector.
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#image-annotation
# download the free icons from https://github.com/Keyamoon/IcoMoon-Free ## Not run: image = sample(dir("~/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10) anno = anno_image(image) draw(anno, test = "png") image[1:5] = "" anno = anno_image(image) draw(anno, test = "some of png") ## End(Not run)# download the free icons from https://github.com/Keyamoon/IcoMoon-Free ## Not run: image = sample(dir("~/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10) anno = anno_image(image) draw(anno, test = "png") image[1:5] = "" anno = anno_image(image) draw(anno, test = "some of png") ## End(Not run)
Joyplot Annotation
anno_joyplot(x, which = c("column", "row"), gp = gpar(fill = "#000000"), scale = 2, transparency = 0.6, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)anno_joyplot(x, which = c("column", "row"), gp = gpar(fill = "#000000"), scale = 2, transparency = 0.6, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)
x |
A matrix or a list. If |
which |
Whether it is a column annotation or a row annotation? |
gp |
Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations. |
scale |
Relative height of the curve. A value higher than 1 increases the height of the curve. |
transparency |
Transparency of the filled colors. Value should be between 0 and 1. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#joyplot-annotation
m = matrix(rnorm(1000), nc = 10) lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")])) anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row") draw(anno, test = "joyplot") anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = 1:10)) draw(anno, test = "joyplot + col") anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", scale = 1) draw(anno, test = "joyplot + scale") m = matrix(rnorm(5000), nc = 50) lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")])) anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = NA), scale = 4) draw(anno, test = "joyplot")m = matrix(rnorm(1000), nc = 10) lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")])) anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row") draw(anno, test = "joyplot") anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = 1:10)) draw(anno, test = "joyplot + col") anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", scale = 1) draw(anno, test = "joyplot + scale") m = matrix(rnorm(5000), nc = 50) lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")])) anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = NA), scale = 4) draw(anno, test = "joyplot")
Lines Annotation
anno_lines(x, which = c("column", "row"), border = TRUE, gp = gpar(), add_points = smooth, smooth = FALSE, pch = 16, size = unit(2, "mm"), pt_gp = gpar(), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)anno_lines(x, which = c("column", "row"), border = TRUE, gp = gpar(), add_points = smooth, smooth = FALSE, pch = 16, size = unit(2, "mm"), pt_gp = gpar(), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL)
x |
The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for lines. The length of each graphic parameter can be 1, or number of columns of |
add_points |
Whether to add points on the lines? |
smooth |
If it is |
pch |
Point type. The length setting is the same as |
size |
Point size, the value should be a |
pt_gp |
Graphic parameters for points. The length setting is the same as |
ylim |
Data ranges. By default it is |
extend |
The extension to both side of |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#lines-annotation
anno = anno_lines(runif(10)) draw(anno, test = "anno_lines") anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3)) draw(anno, test = "matrix") anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3), add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16)) draw(anno, test = "matrix")anno = anno_lines(runif(10)) draw(anno, test = "anno_lines") anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3)) draw(anno, test = "matrix") anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3), add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16)) draw(anno, test = "matrix")
Link Annotation
anno_link(...)anno_link(...)
... |
Pass to |
This function is the same as anno_zoom. It links subsets of rows or columns to a list of graphic regions.
# There is no example NULL# There is no example NULL
Link annotation with labels
anno_mark(at, labels, which = c("column", "row"), side = ifelse(which == "column", "top", "right"), lines_gp = gpar(), labels_gp = gpar(), labels_rot = ifelse(which == "column", 90, 0), padding = unit(1, "mm"), link_width = unit(5, "mm"), link_height = link_width, link_gp = lines_gp, extend = unit(0, "mm"))anno_mark(at, labels, which = c("column", "row"), side = ifelse(which == "column", "top", "right"), lines_gp = gpar(), labels_gp = gpar(), labels_rot = ifelse(which == "column", 90, 0), padding = unit(1, "mm"), link_width = unit(5, "mm"), link_height = link_width, link_gp = lines_gp, extend = unit(0, "mm"))
at |
Numeric index from the original matrix. |
labels |
Corresponding labels. |
which |
Whether it is a column annotation or a row annotation? |
side |
Side of the labels. If it is a column annotation, valid values are "top" and "bottom"; If it is a row annotation, valid values are "left" and "right". |
lines_gp |
Please use |
link_gp |
Graphic settings for the segments. |
labels_gp |
Graphic settings for the labels. |
labels_rot |
Rotations of labels, scalar. |
padding |
Padding between neighbouring labels in the plot. |
link_width |
Width of the segments. |
link_height |
Similar as |
extend |
By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or a |
Sometimes there are many rows or columns in the heatmap and we want to mark some of the rows. This annotation function is used to mark these rows and connect labels and corresponding rows with links.
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#mark-annotation
anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row") draw(anno, index = 1:100, test = "anno_mark") m = matrix(1:1000, byrow = TRUE, nr = 100) anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row") Heatmap(m, cluster_rows = FALSE, cluster_columns = FALSE) + rowAnnotation(mark = anno) Heatmap(m) + rowAnnotation(mark = anno)anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row") draw(anno, index = 1:100, test = "anno_mark") m = matrix(1:1000, byrow = TRUE, nr = 100) anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row") Heatmap(m, cluster_rows = FALSE, cluster_columns = FALSE) + rowAnnotation(mark = anno) Heatmap(m) + rowAnnotation(mark = anno)
Numeric labels annotation
anno_numeric(x, rg = range(x), labels_gp = gpar(), x_convert = NULL, labels_format = NULL, labels_offset = unit(4, "pt"), bg_gp = gpar(fill = "#8080FF", col = "#8080FF"), bar_width = unit(1, "npc") - unit(4, "pt"), round_corners = TRUE, r = unit(0.05, "snpc"), which = c("row", "column"), align_to = "left", width = NULL)anno_numeric(x, rg = range(x), labels_gp = gpar(), x_convert = NULL, labels_format = NULL, labels_offset = unit(4, "pt"), bg_gp = gpar(fill = "#8080FF", col = "#8080FF"), bar_width = unit(1, "npc") - unit(4, "pt"), round_corners = TRUE, r = unit(0.05, "snpc"), which = c("row", "column"), align_to = "left", width = NULL)
x |
A vector of numeric values. |
rg |
Range. A numeric vector of length two. |
labels_gp |
Graphics parameters for labels. |
x_convert |
A function applied on |
labels_format |
A function applied on |
labels_offset |
Offset of labels to the left or right of bars. |
bg_gp |
Graphics parameters for the background bars. |
bar_width |
Width of bars. Note it corresponds to the vertical direction. |
round_corners |
Whether to draw bars with round corners? |
r |
Radius of the round corners. |
which |
Row or column. Currently it only supports row annotation. |
align_to |
Which side bars as well as the labels are aligned to. Values can be "left" or "right". If |
width |
Width of the annotation. |
m = matrix(rnorm(100), 10) x = rnorm(10) Heatmap(m, right_annotation = rowAnnotation(numeric = anno_numeric(x)))m = matrix(rnorm(100), 10) x = rnorm(10) Heatmap(m, right_annotation = rowAnnotation(numeric = anno_numeric(x)))
Barplot Annotation for oncoPrint
anno_oncoprint_barplot(type = NULL, which = c("column", "row"), bar_width = 0.6, beside = FALSE, ylim = NULL, show_fraction = FALSE, axis = TRUE, axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0), width = NULL, height = NULL, border = FALSE)anno_oncoprint_barplot(type = NULL, which = c("column", "row"), bar_width = 0.6, beside = FALSE, ylim = NULL, show_fraction = FALSE, axis = TRUE, axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0), width = NULL, height = NULL, border = FALSE)
type |
A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all. |
which |
Is it a row annotation or a column annotation? |
bar_width |
Width of the bars. |
beside |
Will bars be stacked or be positioned beside each other? |
ylim |
Data range. |
show_fraction |
Whether to show the numbers or the fractions? |
axis |
Whether draw axis? |
axis_param |
Parameters for controlling axis. |
width |
Width of the annotation. |
height |
Height of the annotation. |
border |
Whether draw the border? |
This annotation function should always be used with oncoPrint.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Points Annotation
anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL, ...)anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, axis_param = default_axis_param(which), width = NULL, height = NULL, ...)
x |
The value vector. The value can be a vector or a matrix. The length of the vector or the number of rows of the matrix is taken as the number of the observations of the annotation. |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for points. The length of each graphic parameter can be 1, length of |
pch |
Point type. The length setting is the same as |
size |
Point size, the value should be a |
ylim |
Data ranges. By default it is |
extend |
The extension to both side of |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
... |
Other arguments. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#points-annotation
anno = anno_points(runif(10)) draw(anno, test = "anno_points") anno = anno_points(matrix(runif(20), nc = 2), pch = 1:2) draw(anno, test = "matrix")anno = anno_points(runif(10)) draw(anno, test = "anno_points") anno = anno_points(matrix(runif(20), nc = 2), pch = 1:2) draw(anno, test = "matrix")
Simple Annotation
anno_simple(x, col, na_col = "grey", which = c("column", "row"), border = FALSE, gp = gpar(), pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(), simple_anno_size = ht_opt$simple_anno_size, width = NULL, height = NULL)anno_simple(x, col, na_col = "grey", which = c("column", "row"), border = FALSE, gp = gpar(), pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(), simple_anno_size = ht_opt$simple_anno_size, width = NULL, height = NULL)
x |
The value vector. The value can be a vector or a matrix. The length of the vector or the nrow of the matrix is taken as the number of the observations of the annotation. The value can be numeric or character and NA value is allowed. |
col |
Color that maps to |
na_col |
Color for NA value. |
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
gp |
Graphic parameters for grid borders. The |
pch |
Points/symbols that are added on top of the annotation grids. The value can be numeric or single letters. It can be a vector if |
pt_size |
Size of the points/symbols. It should be a |
pt_gp |
Graphic parameters for points/symbols. The length setting is same as |
simple_anno_size |
size of the simple annotation. |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
The "simple annotation" is the most widely used annotation type which is heatmap-like, where
the grid colors correspond to the values. anno_simple also supports to add points/symbols
on top of the grids where the it can be normal point (when pch is set as numbers) or letters (when
pch is set as single letters).
An annotation function which can be used in HeatmapAnnotation.
anno = anno_simple(1:10) draw(anno, test = "a numeric vector") anno = anno_simple(cbind(1:10, 10:1)) draw(anno, test = "a matrix") anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10)) draw(anno, test = "pch has NA values") anno = anno_simple(1:10, pch = c(rep("A", 5), rep(NA, 5))) draw(anno, test = "pch has NA values") pch = matrix(1:20, nc = 2) pch[sample(length(pch), 10)] = NA anno = anno_simple(cbind(1:10, 10:1), pch = pch) draw(anno, test = "matrix, pch is a matrix with NA values")anno = anno_simple(1:10) draw(anno, test = "a numeric vector") anno = anno_simple(cbind(1:10, 10:1)) draw(anno, test = "a matrix") anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10)) draw(anno, test = "pch has NA values") anno = anno_simple(1:10, pch = c(rep("A", 5), rep(NA, 5))) draw(anno, test = "pch has NA values") pch = matrix(1:20, nc = 2) pch[sample(length(pch), 10)] = NA anno = anno_simple(cbind(1:10, 10:1), pch = pch) draw(anno, test = "matrix, pch is a matrix with NA values")
Summary Annotation
anno_summary(which = c("column", "row"), border = TRUE, bar_width = 0.8, axis = TRUE, axis_param = default_axis_param(which), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, pch = 1, size = unit(2, "mm"), gp = gpar(), width = NULL, height = NULL)anno_summary(which = c("column", "row"), border = TRUE, bar_width = 0.8, axis = TRUE, axis_param = default_axis_param(which), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, pch = 1, size = unit(2, "mm"), gp = gpar(), width = NULL, height = NULL)
which |
Whether it is a column annotation or a row annotation? |
border |
Wether draw borders of the annotation region? |
bar_width |
Relative width of the bars. The value should be smaller than one. |
axis |
Whether to add axis? |
axis_param |
parameters for controlling axis. See |
ylim |
Data ranges. |
extend |
The extension to both side of |
outline |
Whether draw outline of boxplots? |
box_width |
Relative width of boxes. The value should be smaller than one. |
pch |
Point style. |
size |
Point size. |
gp |
Graphic parameters. |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
anno_summary is a special annotation function that it only works for one-column or one-row heatmap.
It shows the summary of the values in the heatmap. If the values in the heatmap is discrete,
the proportion of each level (the sum is normalized to 1) is visualized as stacked barplot. If the heatmap
is split into multiple slices, multiple bars are put in the annotation. If the value is continuous, boxplot is used.
In the barplot, the color schema is used as the same as the heatmap, while for the boxplot, the color needs
to be controlled by gp.
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#summary-annotation
ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm"))) v = sample(letters[1:2], 50, replace = TRUE) split = sample(letters[1:2], 50, replace = TRUE) Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split) ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm"))) v = rnorm(50) Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm"))) v = sample(letters[1:2], 50, replace = TRUE) split = sample(letters[1:2], 50, replace = TRUE) Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split) ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm"))) v = rnorm(50) Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)
Text Annotation
anno_text(x, which = c("column", "row"), gp = gpar(), rot = guess_rot(), just = guess_just(), offset = guess_location(), location = guess_location(), width = NULL, height = NULL, show_name = FALSE)anno_text(x, which = c("column", "row"), gp = gpar(), rot = guess_rot(), just = guess_just(), offset = guess_location(), location = guess_location(), width = NULL, height = NULL, show_name = FALSE)
x |
A vector of text. |
which |
Whether it is a column annotation or a row annotation? |
gp |
Graphic parameters. |
rot |
Rotation of the text, pass to |
just |
Justification of text, pass to |
offset |
Depracated, use |
location |
Position of the text. By default |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
show_name |
Whether to show the annotation name. |
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#text-annotation
anno = anno_text(month.name) draw(anno, test = "month names") anno = anno_text(month.name, gp = gpar(fontsize = 16)) draw(anno, test = "month names with fontsize") anno = anno_text(month.name, gp = gpar(fontsize = 1:12+4)) draw(anno, test = "month names with changing fontsize") anno = anno_text(month.name, which = "row") draw(anno, test = "month names on rows") anno = anno_text(month.name, location = 0, rot = 45, just = "left", gp = gpar(col = 1:12)) draw(anno, test = "with rotations") anno = anno_text(month.name, location = 1, rot = 45, just = "right", gp = gpar(fontsize = 1:12+4)) draw(anno, test = "with rotations")anno = anno_text(month.name) draw(anno, test = "month names") anno = anno_text(month.name, gp = gpar(fontsize = 16)) draw(anno, test = "month names with fontsize") anno = anno_text(month.name, gp = gpar(fontsize = 1:12+4)) draw(anno, test = "month names with changing fontsize") anno = anno_text(month.name, which = "row") draw(anno, test = "month names on rows") anno = anno_text(month.name, location = 0, rot = 45, just = "left", gp = gpar(col = 1:12)) draw(anno, test = "with rotations") anno = anno_text(month.name, location = 1, rot = 45, just = "right", gp = gpar(fontsize = 1:12+4)) draw(anno, test = "with rotations")
Text box annotations
anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"), which = c("row", "column"), by = "anno_link", side = c("right", "left"), ...)anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"), which = c("row", "column"), by = "anno_link", side = c("right", "left"), ...)
align_to |
It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same length as heatmap rows, or a list of row indices. It does not necessarily include all row indices. |
text |
The corresponding texts. The value should be a list of texts. To control graphics parameters of texts in the boxes, The value of |
background_gp |
Graphics for the background. |
which |
Only "row" is allowed. |
by |
Are text boxed arranged by |
side |
Side of the annotation to the heatmap. |
... |
Pass to |
require(circlize) mat = matrix(rnorm(100*10), nrow = 100) split = sample(letters[1:10], 100, replace = TRUE) text = lapply(unique(split), function(x) { data.frame(month.name, col = rand_color(12, friendly = TRUE), fontsize = runif(12, 6, 14)) }) names(text) = unique(split) Heatmap(mat, cluster_rows = FALSE, row_split = split, right_annotation = rowAnnotation(wc = anno_textbox(split, text)) )require(circlize) mat = matrix(rnorm(100*10), nrow = 100) split = sample(letters[1:10], 100, replace = TRUE) text = lapply(unique(split), function(x) { data.frame(month.name, col = rand_color(12, friendly = TRUE), fontsize = runif(12, 6, 14)) }) names(text) = unique(split) Heatmap(mat, cluster_rows = FALSE, row_split = split, right_annotation = rowAnnotation(wc = anno_textbox(split, text)) )
Zoom annotation
anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() }, which = c("column", "row"), side = ifelse(which == "column", "top", "right"), size = NULL, gap = unit(1, "mm"), link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(), extend = unit(0, "mm"), width = NULL, height = NULL, internal_line = TRUE)anno_zoom(align_to, panel_fun = function(index, nm = NULL) { grid.rect() }, which = c("column", "row"), side = ifelse(which == "column", "top", "right"), size = NULL, gap = unit(1, "mm"), link_width = unit(5, "mm"), link_height = link_width, link_gp = gpar(), extend = unit(0, "mm"), width = NULL, height = NULL, internal_line = TRUE)
align_to |
It defines how the boxes correspond to the rows or the columns in the heatmap. If the value is a list of indices, each box corresponds to the rows or columns with indices in one vector in the list. If the value is a categorical variable (e.g. a factor or a character vector) that has the same length as the rows or columns in the heatmap, each box corresponds to the rows/columns in each level in the categorical variable. |
panel_fun |
A self-defined function that defines how to draw graphics in the box. The function must have a |
which |
Whether it is a column annotation or a row annotation? |
side |
Side of the boxes If it is a column annotation, valid values are "top" and "bottom"; If it is a row annotation, valid values are "left" and "right". |
size |
The size of boxes. It can be pure numeric that they are treated as relative fractions of the total height/width of the heatmap. The value of |
gap |
Gaps between boxes. |
link_gp |
Graphic settings for the segments. |
link_width |
Width of the segments. |
link_height |
Similar as |
extend |
By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or a |
width |
Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
height |
Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
internal_line |
Internally used. |
anno_zoom creates several plotting regions (boxes) which can be corresponded to subsets of rows/columns in the
heatmap.
An annotation function which can be used in HeatmapAnnotation.
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#zoom-annotation
set.seed(123) m = matrix(rnorm(100*10), nrow = 100) subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10)) rg = range(m) panel_fun = function(index, nm) { pushViewport(viewport(xscale = rg, yscale = c(0, 2))) grid.rect() grid.xaxis(gp = gpar(fontsize = 8)) grid.boxplot(m[index, ], pos = 1, direction = "horizontal") grid.text(paste("distribution of group", nm), mean(rg), y = 1.9, just = "top", default.units = "native", gp = gpar(fontsize = 10)) popViewport() } anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun, size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm")) Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup)set.seed(123) m = matrix(rnorm(100*10), nrow = 100) subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10)) rg = range(m) panel_fun = function(index, nm) { pushViewport(viewport(xscale = rg, yscale = c(0, 2))) grid.rect() grid.xaxis(gp = gpar(fontsize = 8)) grid.boxplot(m[index, ], pos = 1, direction = "horizontal") grid.text(paste("distribution of group", nm), mean(rg), y = 1.9, just = "top", default.units = "native", gp = gpar(fontsize = 10)) popViewport() } anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun, size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm")) Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup)
Grob for Annotation Axis
annotation_axis_grob(at = NULL, labels = at, labels_rot = 0, gp = gpar(), side = "left", facing = "outside", direction = "normal", scale = NULL)annotation_axis_grob(at = NULL, labels = at, labels_rot = 0, gp = gpar(), side = "left", facing = "outside", direction = "normal", scale = NULL)
at |
Break values. If it is not specified, it is inferred from data scale in current viewport. |
labels |
Corresponding labels. |
labels_rot |
Rotations of labels. |
gp |
Graphic parameters. |
side |
side of the axis of the annotation viewport. |
facing |
Facing of the axis. |
direction |
Direction of the axis. Value should be "normal" or "reverse". |
scale |
The data scale. If it is |
A grob object.
gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "left", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "left", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "left", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "left", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "right", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "right", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "right", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "right", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 90, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 45, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "top", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "bottom", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "bottom", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "bottom", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "bottom", facing = "inside"') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(labels_rot = 0, side = "left", facing = "outside") grid.rect() grid.text('side = "left", facing = "outside"') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(side = "left", direction = "reverse") grid.rect() grid.text('side = "left", direction = "reverse') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(side = "bottom", direction = "reverse") grid.rect() grid.text('side = "bottom", directio = "reverse"') grid.draw(gb) popViewport()gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "left", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "left", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "left", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "left", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "right", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "right", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, side = "right", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "right", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 90, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 45, side = "top", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "top", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "top", facing = "inside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "bottom", facing = "outside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "bottom", facing = "outside"') grid.draw(gb) popViewport() gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, side = "bottom", facing = "inside") grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) grid.rect() grid.text('side = "bottom", facing = "inside"') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(labels_rot = 0, side = "left", facing = "outside") grid.rect() grid.text('side = "left", facing = "outside"') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(side = "left", direction = "reverse") grid.rect() grid.text('side = "left", direction = "reverse') grid.draw(gb) popViewport() grid.newpage() pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6)) gb = annotation_axis_grob(side = "bottom", direction = "reverse") grid.rect() grid.text('side = "bottom", directio = "reverse"') grid.draw(gb) popViewport()
Size of the Annotation Legends
## S4 method for signature 'HeatmapList' annotation_legend_size(object, legend_list = list(), ...)## S4 method for signature 'HeatmapList' annotation_legend_size(object, legend_list = list(), ...)
object |
a |
legend_list |
A list of self-defined legend, should be wrapped into |
... |
Other arguments. |
Internally, all annotation legends are packed by packLegend as a single grob object.
This function is only for internal use.
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Constructor of AnnotationFunction Class
AnnotationFunction(fun, fun_name = "", which = c("column", "row"), cell_fun = NULL, var_import = list(), n = NA, data_scale = c(0, 1), subset_rule = list(), subsettable = length(subset_rule) > 0, show_name = TRUE, width = NULL, height = NULL)AnnotationFunction(fun, fun_name = "", which = c("column", "row"), cell_fun = NULL, var_import = list(), n = NA, data_scale = c(0, 1), subset_rule = list(), subsettable = length(subset_rule) > 0, show_name = TRUE, width = NULL, height = NULL)
fun |
A function which defines how to draw the annotation. See **Details** section. |
fun_name |
The name of the function. It is only used for printing the object. |
which |
Whether it is drawn as a column annotation or a row annotation? |
cell_fun |
A simplified version of |
var_import |
The names of the variables or the variable themselves that the annotation function depends on. See **Details** section. |
n |
Number of observations in the annotation. It is not mandatory, but it is better to provide this information so that the higher order |
data_scale |
The data scale on the data axis (y-axis for column annotation and x-axis for row annotation). It is only used when |
subset_rule |
The rule of subsetting variables in |
subsettable |
Whether the object is subsettable? |
show_name |
It is used to turn off the drawing of annotation names in |
width |
The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit. Since the |
height |
The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit. |
In the package, we have implemted quite a lot annotation functions by AnnotationFunction constructor:
anno_empty, anno_image, anno_points, anno_lines, anno_barplot, anno_boxplot, anno_histogram,
anno_density, anno_joyplot, anno_horizon, anno_text and anno_mark. These built-in annotation functions
support as both row annotations and column annotations and they are are all subsettable.
The build-in annotation functions are already enough for most of the analysis, nevertheless, if users want to know more about how to construct the AnnotationFunction class manually, they can refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#implement-new-annotation-functions.
A AnnotationFunction-class object which can be used in HeatmapAnnotation.
x = 1:10 anno1 = AnnotationFunction( fun = function(index, k, n) { n = length(index) pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(0, 10))) grid.rect() grid.points(1:n, x[index], default.units = "native") if(k == 1) grid.yaxis() popViewport() }, var_import = list(x = x), n = 10, subsettable = TRUE, height = unit(2, "cm") ) m = rbind(1:10, 11:20) Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1)) Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1), column_km = 2)x = 1:10 anno1 = AnnotationFunction( fun = function(index, k, n) { n = length(index) pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(0, 10))) grid.rect() grid.points(1:n, x[index], default.units = "native") if(k == 1) grid.yaxis() popViewport() }, var_import = list(x = x), n = 10, subsettable = TRUE, height = unit(2, "cm") ) m = rbind(1:10, 11:20) Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1)) Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1), column_km = 2)
The AnnotationFunction Class
The heatmap annotation is basically graphics aligned to the heatmap columns or rows. There is no restriction for the graphic types, e.g. it can be heatmap-like annotation or points. Here the AnnotationFunction class is designed for creating complex and flexible annotation graphics. As the main part of the class, it uses a user-defined function to define the graphics. It also keeps information of the size of the plotting regions of the annotation. And most importantly, it allows subsetting to the annotation to draw a subset of the graphics, which is the base for the splitting of the annotations.
See AnnotationFunction constructor for details.
# There is no example NULL# There is no example NULL
Attach heatmap annotations to the heatmap
## S4 method for signature 'Heatmap' attach_annotation(object, ha, side = c("top", "bottom", "left", "right"), gap = unit(1, "points"))## S4 method for signature 'Heatmap' attach_annotation(object, ha, side = c("top", "bottom", "left", "right"), gap = unit(1, "points"))
object |
A |
ha |
A |
side |
Which side of the heatmap. Value should be in "top", "bottom", "left", "right". |
gap |
Space between the two heatmap annotations. |
m = matrix(rnorm(100), 10) ht = Heatmap(m) ha = HeatmapAnnotation(foo = 1:10) ht = attach_annotation(ht, ha) ht ha2 = HeatmapAnnotation(bar = letters[1:10]) ht = attach_annotation(ht, ha2) htm = matrix(rnorm(100), 10) ht = Heatmap(m) ha = HeatmapAnnotation(foo = 1:10) ht = attach_annotation(ht, ha) ht ha2 = HeatmapAnnotation(bar = letters[1:10]) ht = attach_annotation(ht, ha2) ht
Draw 3D bars
bar3D(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black")bar3D(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black")
x |
x coordinate of the center point in the bottom face. |
y |
y coordinate of the center point in the bottom face. |
w |
Width of the botton face. |
h |
Height of the botton face. |
l |
Length of the bars (in the z-direction). |
theta |
The angle for the projection. |
default.units |
Units. |
fill |
Filled colors for the bars. |
col |
Border colors. |
grid.newpage() bar3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)grid.newpage() bar3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
Bin the genome
bin_genome(species = "hg19", bins = 2000, bin_size = NULL, ...)bin_genome(species = "hg19", bins = 2000, bin_size = NULL, ...)
species |
Abbreviation of the genome, pass to |
bins |
Number of bins. The final number of bins is approximately equal to it. |
bin_size |
Size of the bins. If |
... |
All pass to |
A GRanges object of the genomic bins.
# There is no example NULL# There is no example NULL
Concatenate A List of ColorMapping objects
## S3 method for class 'ColorMapping' c(..., name = NULL)## S3 method for class 'ColorMapping' c(..., name = NULL)
... |
A list of |
name |
Name of the new merged color mapping. |
Only discrete color mappings can be concatenated.
cm1 = ColorMapping(colors = c("A" = "red", "B" = "black")) cm2 = ColorMapping(colors = c("B" = "blue", "C" = "green")) c(cm1, cm2)cm1 = ColorMapping(colors = c("A" = "red", "B" = "black")) cm2 = ColorMapping(colors = c("B" = "blue", "C" = "green")) c(cm1, cm2)
Concatenate Heatmap Annotations
## S3 method for class 'HeatmapAnnotation' c(..., gap = unit(1, "points"))## S3 method for class 'HeatmapAnnotation' c(..., gap = unit(1, "points"))
... |
|
gap |
Gap between the groups of annotations. |
The heatmap annotations should have same number of observations.
ha1 = HeatmapAnnotation(foo = 1:10) ha2 = HeatmapAnnotation(bar = anno_points(10:1)) ha = c(ha1, ha2) ha ha3 = HeatmapAnnotation(sth = cbind(1:10, 10:1)) ha = c(ha1, ha2, ha3, gap = unit(c(1, 4), "mm")) haha1 = HeatmapAnnotation(foo = 1:10) ha2 = HeatmapAnnotation(bar = anno_points(10:1)) ha = c(ha1, ha2) ha ha3 = HeatmapAnnotation(sth = cbind(1:10, 10:1)) ha = c(ha1, ha2, ha3, gap = unit(c(1, 4), "mm")) ha
Cluster only between Groups
cluster_between_groups(mat, factor)cluster_between_groups(mat, factor)
mat |
A matrix where clustering is applied on columns. |
factor |
A categorical vector. |
The clustering is only applied between groups and inside a group, the order is unchanged.
A dendrogram object.
m = matrix(rnorm(120), nc = 12) colnames(m) = letters[1:12] fa = rep(c("a", "b", "c"), times = c(2, 4, 6)) dend = cluster_between_groups(m, fa) grid.dendrogram(dend, test = TRUE)m = matrix(rnorm(120), nc = 12) colnames(m) = letters[1:12] fa = rep(c("a", "b", "c"), times = c(2, 4, 6)) dend = cluster_between_groups(m, fa) grid.dendrogram(dend, test = TRUE)
Cluster within and between Groups
cluster_within_group(mat, factor)cluster_within_group(mat, factor)
mat |
A matrix where clustering is applied on columns. |
factor |
A categorical vector. |
The clustering is firstly applied in each group, then clustering is applied
to group means. The within-group dendrograms and between-group dendrogram
are finally connected by merge_dendrogram.
In the final dendrogram, the within group dendrograms are enforced to be flat lines to emphasize that the within group dendrograms have no sense to compare to between-group dendrogram.
A dendrogram object. The order of columns can be retrieved by order.dendrogram.
m = matrix(rnorm(120), nc = 12) colnames(m) = letters[1:12] fa = rep(c("a", "b", "c"), times = c(2, 4, 6)) dend = cluster_within_group(m, fa) grid.dendrogram(dend, test = TRUE)m = matrix(rnorm(120), nc = 12) colnames(m) = letters[1:12] fa = rep(c("a", "b", "c"), times = c(2, 4, 6)) dend = cluster_within_group(m, fa) grid.dendrogram(dend, test = TRUE)
Draw Legend Based on Color Mapping
## S4 method for signature 'ColorMapping' color_mapping_legend(object, plot = TRUE, ..., color_bar = object@type, title = object@name, title_gp = gpar(fontsize = 10, fontface = "bold"), title_position = "topleft", grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), tick_length = unit(0.8, "mm"), border = NULL, at = object@levels, labels = at, labels_gp = gpar(fontsize = 10), labels_rot = 0, nrow = NULL, ncol = 1, by_row = FALSE, legend_gp = gpar(), legend_height = NULL, legend_width = NULL, legend_direction = c("vertical", "horizontal"), break_dist = NULL, graphics = NULL, param = NULL)## S4 method for signature 'ColorMapping' color_mapping_legend(object, plot = TRUE, ..., color_bar = object@type, title = object@name, title_gp = gpar(fontsize = 10, fontface = "bold"), title_position = "topleft", grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), tick_length = unit(0.8, "mm"), border = NULL, at = object@levels, labels = at, labels_gp = gpar(fontsize = 10), labels_rot = 0, nrow = NULL, ncol = 1, by_row = FALSE, legend_gp = gpar(), legend_height = NULL, legend_width = NULL, legend_direction = c("vertical", "horizontal"), break_dist = NULL, graphics = NULL, param = NULL)
object |
A |
plot |
Whether to plot or just return the legend object? |
... |
Pass to |
color_bar |
"continous" or "discrete". It controls whether to show the discrete legend for the continuous color mapping. |
title |
Title of the legend, by default it is the name of the legend. |
title_gp |
Graphical parameters for legend title. |
title_position |
Position of the title. See |
grid_height |
Height of each legend grid. Pass to |
grid_width |
Width of each legend grid. Pass to |
tick_length |
Length of the ticks on the continuous legends. Value should be a |
border |
Color for legend grid borders. Pass to |
at |
Break values of the legend. By default it is the levels in the |
labels |
Labels corresponding to break values. |
labels_gp |
Graphcial parameters for legend labels. |
labels_rot |
Rotation of labels. |
nrow |
Pass to |
ncol |
Pass to |
by_row |
Pass to |
legend_gp |
Graphic parameters for legend. |
legend_height |
Height of the legend body. It only works when |
legend_width |
Width of the legend body. It only works when |
legend_direction |
When |
break_dist |
A zooming factor to control relative distance of two neighbouring break values.The length of it should be |
graphics |
Internally used. |
param |
All the legend-related parameters can be specified as a single list. |
The legend is constructed by Legend.
A Legends-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Constructor Method for ColorMapping Class
ColorMapping(name, colors = NULL, levels = NULL, col_fun = NULL, breaks = NULL, na_col = "#FFFFFF", full_col = NULL)ColorMapping(name, colors = NULL, levels = NULL, col_fun = NULL, breaks = NULL, na_col = "#FFFFFF", full_col = NULL)
name |
Name for this color mapping. The name is automatically generated if it is not specified. |
colors |
Discrete colors. |
levels |
Levels that correspond to |
col_fun |
Color mapping function that maps continuous values to colors. |
breaks |
Breaks for the continuous color mapping. If |
na_col |
Colors for |
full_col |
A super set of |
colors and levels are used for discrete color mapping, col_fun and
breaks are used for continuous color mapping.
A ColorMapping-class object.
Zuguang Gu <[email protected]>
cm = ColorMapping(colors = c("A" = "red", "B" = "black")) cm require(circlize) col_fun = colorRamp2(c(0, 1), c("white", "red")) cm = ColorMapping(col_fun = col_fun)cm = ColorMapping(colors = c("A" = "red", "B" = "black")) cm require(circlize) col_fun = colorRamp2(c(0, 1), c("white", "red")) cm = ColorMapping(col_fun = col_fun)
Class for Color Mapping
The ColorMapping-class handles color mapping for discrete values and continuous values.
Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting
a color mapping function.
The ColorMapping-class provides following methods:
ColorMapping: contructor methods.
map_to_colors,ColorMapping-method: mapping values to colors.
color_mapping_legend,ColorMapping-method: draw legend or get legend as an object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Method dispatch page for column_dend.
column_dend can be dispatched on following classes:
column_dend,Heatmap-method, Heatmap-class class method
column_dend,HeatmapList-method, HeatmapList-class class method
# no example NULL# no example NULL
Get Column Dendrograms from a Heatmap
## S4 method for signature 'Heatmap' column_dend(object, on_slice = FALSE)## S4 method for signature 'Heatmap' column_dend(object, on_slice = FALSE)
object |
A |
on_slice |
If the value is TRUE, it returns the dendrogram on the slice level. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) column_dend(ht) ht = Heatmap(mat, column_km = 2) ht = draw(ht) column_dend(ht)mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) column_dend(ht) ht = Heatmap(mat, column_km = 2) ht = draw(ht) column_dend(ht)
Get Column Dendrograms from a hHeatmap List
## S4 method for signature 'HeatmapList' column_dend(object, name = NULL, on_slice = FALSE)## S4 method for signature 'HeatmapList' column_dend(object, name = NULL, on_slice = FALSE)
object |
A |
name |
Name of a specific heatmap. |
on_slice |
If the value is TRUE, it returns the dendrogram on the slice level. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list) ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2) ht_list = draw(ht_list) column_dend(ht_list) column_dend(ht_list, on_slice = TRUE) ht_list = Heatmap(mat) %v% Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list) ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list)mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list) ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2) ht_list = draw(ht_list) column_dend(ht_list) column_dend(ht_list, on_slice = TRUE) ht_list = Heatmap(mat) %v% Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list) ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) column_dend(ht_list)
Method dispatch page for column_order.
column_order can be dispatched on following classes:
column_order,Heatmap-method, Heatmap-class class method
column_order,HeatmapList-method, HeatmapList-class class method
# no example NULL# no example NULL
Get Column Order from a Aeatmap List
## S4 method for signature 'Heatmap' column_order(object)## S4 method for signature 'Heatmap' column_order(object)
object |
A |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) column_order(ht) ht = Heatmap(mat, column_km = 2) ht = draw(ht) column_order(ht)mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) column_order(ht) ht = Heatmap(mat, column_km = 2) ht = draw(ht) column_order(ht)
Get Column Order from a Heatmap List
## S4 method for signature 'HeatmapList' column_order(object, name = NULL)## S4 method for signature 'HeatmapList' column_order(object, name = NULL)
object |
A |
name |
Name of a specific heatmap. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat) %v% Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list)mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat) %v% Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list) ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) column_order(ht_list)
Construct Column Annotations
columnAnnotation(...)columnAnnotation(...)
... |
Pass to |
The function is identical to
HeatmapAnnotation(..., which = "column")
A HeatmapAnnotation-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Degrees of the Combination sets
comb_degree(m)comb_degree(m)
m |
A combination matrix returned by |
The degree for a combination set is the number of sets that are selected.
A vector of degrees of the combination sets.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_degree(m)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_degree(m)
Names of the Combination sets
comb_name(m, readable = FALSE)comb_name(m, readable = FALSE)
m |
A combination matrix returned by |
readable |
Whether the combination represents as e.g. "A&B&C". |
The name of the combination sets are formatted as a string
of binary bits. E.g. for three sets of "a", "b", "c", the combination
set with name "101" corresponds to select set a, not select set b
and select set c. The definition of "select" depends on the value of
mode from make_comb_mat.
A vector of names of the combination sets.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_name(m) comb_name(m, readable = TRUE)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_name(m) comb_name(m, readable = TRUE)
Sizes of the Combination sets
comb_size(m, degree = NULL)comb_size(m, degree = NULL)
m |
A combination matrix returned by |
degree |
degree of the intersection. The value can be a vector. |
A vector of sizes of the combination sets.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_size(m)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) comb_size(m)
Compare heatmaps between stats::heatmap() and ComplexHeatmap::heatmap()
compare_heatmap(...)compare_heatmap(...)
... |
The same set of arguments passed to |
The function plots two heatmaps, one by stats::heatmap and one by ComplexHeatmap::heatmap.
Users can see the difference between the two implementations.
mat = matrix(rnorm(100), 10) compare_heatmap(mat)mat = matrix(rnorm(100), 10) compare_heatmap(mat)
Compare heatmaps between gplots::heatmap.2() and ComplexHeatmap::heatmap()
compare_heatmap.2(...)compare_heatmap.2(...)
... |
The same set of arguments passed to |
The function plots two heatmaps, one by gplots::heatmap.2 and one by ComplexHeatmap::heatmap.2.
Users can see the difference between the two implementations.
mat = matrix(rnorm(100), 10) compare_heatmap.2(mat)mat = matrix(rnorm(100), 10) compare_heatmap.2(mat)
Compare heatmaps between pheatmap::pheatmap() and ComplexHeatmap::pheatmap()
compare_pheatmap(...)compare_pheatmap(...)
... |
The same set of arguments passed to |
The function plots two heatmaps, one by pheatmap::pheatmap and one by ComplexHeatmap::pheatmap.
Users can see the difference between the two implementations.
mat = matrix(rnorm(100), 10) compare_pheatmap(mat)mat = matrix(rnorm(100), 10) compare_pheatmap(mat)
Complement Set Size
complement_size(m)complement_size(m)
m |
A combination matrix returned by |
If there is no complement set, it returns zero.
# There is no example NULL# There is no example NULL
Method dispatch page for component_height.
component_height can be dispatched on following classes:
component_height,HeatmapList-method, HeatmapList-class class method
component_height,Heatmap-method, Heatmap-class class method
# no example NULL# no example NULL
Heights of Heatmap Components
## S4 method for signature 'Heatmap' component_height(object, k = HEATMAP_LAYOUT_COLUMN_COMPONENT)## S4 method for signature 'Heatmap' component_height(object, k = HEATMAP_LAYOUT_COLUMN_COMPONENT)
object |
A |
k |
Which components in the heatmap. The value should numeric indices or the names of the corresponding column component. See **Detials**. |
All column components are: column_title_top, column_dend_top, column_names_top,
column_anno_top, heatmap_body, column_anno_bottom, column_names_bottom,
column_dend_bottom, column_title_bottom.
This function is only for internal use.
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Height of Heatmap List Components
## S4 method for signature 'HeatmapList' component_height(object, k = HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT)## S4 method for signature 'HeatmapList' component_height(object, k = HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT)
object |
A |
k |
Which component in the heatmap list. Values are in |
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Method dispatch page for component_width.
component_width can be dispatched on following classes:
component_width,HeatmapList-method, HeatmapList-class class method
component_width,Heatmap-method, Heatmap-class class method
# no example NULL# no example NULL
Widths of Heatmap Components
## S4 method for signature 'Heatmap' component_width(object, k = HEATMAP_LAYOUT_ROW_COMPONENT)## S4 method for signature 'Heatmap' component_width(object, k = HEATMAP_LAYOUT_ROW_COMPONENT)
object |
A |
k |
Which components in the heatmap. The value should numeric indices or the names of the corresponding row component. See **Detials**. |
All row components are: row_title_left, row_dend_left, row_names_left, row_anno_left,
heatmap_body, row_anno_right, row_names_right, row_dend_right, row_title_right.
This function is only for internal use.
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Width of Heatmap List Components
## S4 method for signature 'HeatmapList' component_width(object, k = HEATMAP_LIST_LAYOUT_ROW_COMPONENT)## S4 method for signature 'HeatmapList' component_width(object, k = HEATMAP_LIST_LAYOUT_ROW_COMPONENT)
object |
A |
k |
Which component in the heatmap list. Values are in |
This function is only for internal use.
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Copy the AnnotationFunction Object
## S4 method for signature 'AnnotationFunction' copy_all(object)## S4 method for signature 'AnnotationFunction' copy_all(object)
object |
The |
In AnnotationFunction-class, there is an environment which
stores some external variables for the annotation function (specified by the
var_import argument when constructing the AnnotationFunction-class
object. This copy_all,AnnotationFunction-method hard copies all the
variables into a new isolated environment.
The environment is at object@var_env.
# There is no example NULL# There is no example NULL
Method dispatch page for copy_all.
copy_all can be dispatched on following classes:
copy_all,AnnotationFunction-method, AnnotationFunction-class class method
copy_all,SingleAnnotation-method, SingleAnnotation-class class method
# no example NULL# no example NULL
Copy the SingleAnnotation object
## S4 method for signature 'SingleAnnotation' copy_all(object)## S4 method for signature 'SingleAnnotation' copy_all(object)
object |
The |
Since the SingleAnnotation object always contains an AnnotationFunction-class object,
it calls copy_all,AnnotationFunction-method to hard copy the variable environment.
# There is no example NULL# There is no example NULL
Decorate Heatmap Annotation
decorate_annotation(annotation, code, slice = 1, envir = new.env(parent = parent.frame()))decorate_annotation(annotation, code, slice = 1, envir = new.env(parent = parent.frame()))
annotation |
Name of the annotation. |
code |
Code that adds graphics in the selected heatmap annotation. |
slice |
Index of the row slices or the column slice in the heatmap. |
envir |
Where to look for variables inside |
There is a viewport for every column annotation and row annotation.
This function contructs the name of the viewport,
goes to the viewport by seekViewport, runs code
to that viewport, and finally goes back to the original viewport.
The function returns no value.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
set.seed(123) ha1 = HeatmapAnnotation(df = data.frame(type = rep(letters[1:2], 5))) ha2 = rowAnnotation(point = anno_points(runif(10), which = "row")) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2, top_annotation = ha1) + ha2 decorate_annotation("type", { grid.circle(x = unit(c(0.2, 0.4, 0.6, 0.8), "npc"), gp = gpar(fill = "#FF000080")) }) decorate_annotation("point", { grid.rect(gp = gpar(fill = "#FF000080")) }, slice = 2)set.seed(123) ha1 = HeatmapAnnotation(df = data.frame(type = rep(letters[1:2], 5))) ha2 = rowAnnotation(point = anno_points(runif(10), which = "row")) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2, top_annotation = ha1) + ha2 decorate_annotation("type", { grid.circle(x = unit(c(0.2, 0.4, 0.6, 0.8), "npc"), gp = gpar(fill = "#FF000080")) }) decorate_annotation("point", { grid.rect(gp = gpar(fill = "#FF000080")) }, slice = 2)
Decorate Heatmap Column Dendrograms
decorate_column_dend(..., envir = new.env(parent = parent.frame()))decorate_column_dend(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
Where to look for variables inside |
This is a wrapper function which pre-defined which argument in decorate_dend.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Column Names
decorate_column_names(..., envir = new.env(parent = parent.frame()))decorate_column_names(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
Where to look for variables inside |
This is a helper function which pre-defined which argument in decorate_dimnames.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Column Titles
decorate_column_title(..., envir = new.env(parent = parent.frame()))decorate_column_title(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
Where to look for variables inside |
This is a helper function which pre-defined which argument in decorate_title.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Dendrograms
decorate_dend(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))decorate_dend(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))
heatmap |
Name of the heatmap. |
code |
Code that adds graphics in the selected heatmap dendrogram. |
slice |
Index of the row slice or column slice in the heatmap. |
which |
Is the dendrogram on rows or on columns? |
envir |
Where to look for variables inside |
If you know the number of leaves in the dendrogram, it is simple to calculate the position of every leave in the dendrogram. E.g., for the column dendrogram, the i^th leave is located at:
# assume nc is the number of columns in the column slice
unit((i-0.5)/nc, "npc")
This function returns no value.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2) decorate_dend("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2) decorate_dend("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)
Decorate Heatmap Dimension Names
decorate_dimnames(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))decorate_dimnames(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))
heatmap |
Name of the heatmap. |
code |
Code that adds graphics in the selected viewport. |
slice |
Index of the row slice or column slice in the heatmap. |
which |
on rows or on columns? |
envir |
where to look for variables inside |
If you know the dimensions of the matrix, it is simple to calculate the position of every row name or column name in the heatmap. E.g., for the column column, the i^th name is located at:
# assume nc is the number of columns in the column slice
unit((i-0.5)/nc, "npc")
The function returns no value.
Zuguang Gu <[email protected]>
set.seed(123) mat = matrix(rnorm(100), 10) rownames(mat) = letters[1:10] colnames(mat) = LETTERS[1:10] Heatmap(mat, name = "mat", km = 2) decorate_dimnames("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)set.seed(123) mat = matrix(rnorm(100), 10) rownames(mat) = letters[1:10] colnames(mat) = LETTERS[1:10] Heatmap(mat, name = "mat", km = 2) decorate_dimnames("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)
Decorate Heatmap Bodies
decorate_heatmap_body(heatmap, code, slice = 1, row_slice = slice, column_slice = 1, envir = new.env(parent = parent.frame()))decorate_heatmap_body(heatmap, code, slice = 1, row_slice = slice, column_slice = 1, envir = new.env(parent = parent.frame()))
heatmap |
Name of the heatmap which is set as |
code |
Code that adds graphics in the selected heatmap body. |
slice |
Index of the row slice in the heatmap. |
row_slice |
Index of the row slice in the heatmap. |
column_slice |
Index of the column slice in the heatmap. |
envir |
Where to look for variables inside |
There is a viewport for each slice in each heatmap.
This function contructs the name of the viewport,
goes to the viewport by seekViewport, runs the code
to that viewport and finally goes back to the original viewport.
This function returns no value.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat") decorate_heatmap_body("mat", { grid.circle(gp = gpar(fill = "#FF000080")) })set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat") decorate_heatmap_body("mat", { grid.circle(gp = gpar(fill = "#FF000080")) })
Decorate Heatmap Row Dendrograms
decorate_row_dend(..., envir = new.env(parent = parent.frame()))decorate_row_dend(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
Where to look for variables inside |
This is a helper function which pre-defined which argument in decorate_dend.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Row Names
decorate_row_names(..., envir = new.env(parent = parent.frame()))decorate_row_names(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
wWhere to look for variables inside |
This is a helper function which pre-defined which argument in decorate_dimnames.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Row Titles
decorate_row_title(..., envir = new.env(parent = parent.frame()))decorate_row_title(..., envir = new.env(parent = parent.frame()))
... |
Pass to |
envir |
Where to look for variables inside |
This is a helper function which pre-defined which argument in decorate_title.
The function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Decorate Heatmap Titles
decorate_title(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))decorate_title(heatmap, code, slice = 1, which = c("column", "row"), envir = new.env(parent = parent.frame()))
heatmap |
Name of the heatmap. |
code |
Code that adds graphics in the selected viewport. |
slice |
Index of the row slice or column slice in the heatmap. |
which |
Is it a row title or a column title? |
envir |
Where to look for variables inside |
There is a viewport for row titles and column title in the heatmap.
This function contructs the name of the viewport,
goes to the viewport by seekViewport , runs code
to that viewport and finally goes back to the original viewport.
The function returns no value.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-decoration.html
set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2) decorate_title("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)set.seed(123) Heatmap(matrix(rnorm(100), 10), name = "mat", km = 2) decorate_title("mat", { grid.rect(gp = gpar(fill = "#FF000080")) }, which = "row", slice = 2)
The Default Parameters for Annotation Axis
default_axis_param(which)default_axis_param(which)
which |
Whether it is for column annotation or row annotation? |
There are following parameters for the annotation axis:
The breaks of axis. By default it is automatically inferred.
The corresponding axis labels.
The rotation of the axis labels.
Graphc parameters of axis labels. The value should be a unit object.
If it is for column annotation, the value should only be one of left and right. If it is for row annotation, the value should only be one of top and bottom.
Whether the axis faces to the outside of the annotation region or inside. Sometimes when appending more than one heatmaps, the axes of column annotations of one heatmap might overlap to the neighbouring heatmap, setting facing to inside may invoild it.
The direction of the axis. Value should be "normal" or "reverse".
All the parameters are passed to annotation_axis_grob to construct an axis grob.
default_axis_param("column") default_axis_param("row")default_axis_param("column") default_axis_param("row")
Default get_type for oncoPrint()
default_get_type(x)default_get_type(x)
x |
A strings which encode multiple altertations. |
It recognizes following separators: ;:,|.
# There is no example NULL# There is no example NULL
Height of the Dendrograms
dend_heights(x)dend_heights(x)
x |
a |
# There is no example NULL# There is no example NULL
Coordinates of the Dendrogram
dend_xy(dend)dend_xy(dend)
dend |
a |
dend will be processed by adjust_dend_by_x if it is processed yet.
A list of leave positions (x) and dendrogram height (y).
m = matrix(rnorm(100), 10) dend1 = as.dendrogram(hclust(dist(m))) dend_xy(dend1) dend1 = adjust_dend_by_x(dend1, sort(runif(10))) dend_xy(dend1) dend1 = adjust_dend_by_x(dend1, unit(1:10, "cm")) dend_xy(dend1)m = matrix(rnorm(100), 10) dend1 = as.dendrogram(hclust(dist(m))) dend_xy(dend1) dend1 = adjust_dend_by_x(dend1, sort(runif(10))) dend_xy(dend1) dend1 = adjust_dend_by_x(dend1, unit(1:10, "cm")) dend_xy(dend1)
Grob for Dendrogram
dendrogramGrob(dend, facing = c("bottom", "top", "left", "right"), order = c("normal", "reverse"), gp = gpar())dendrogramGrob(dend, facing = c("bottom", "top", "left", "right"), order = c("normal", "reverse"), gp = gpar())
dend |
A |
facing |
Facing of the dendrogram. |
order |
If it is set to |
gp |
Graphic parameters for the dendrogram segments. If any of |
If dend has not been processed by adjust_dend_by_x, internally adjust_dend_by_x is called
to add x attributes to each node/leaf.
A grob object which is contructed by segmentsGrob.
# There is no example NULL# There is no example NULL
Visualize Density Distribution by Heatmap
densityHeatmap(data, density_param = list(na.rm = TRUE), col = rev(brewer.pal(11, "Spectral")), color_space = "LAB", ylab = deparse(substitute(data)), column_title = paste0("Density heatmap of ", deparse(substitute(data))), title = column_title, ylim = NULL, range = ylim, title_gp = gpar(fontsize = 14), ylab_gp = gpar(fontsize = 12), tick_label_gp = gpar(fontsize = 10), quantile_gp = gpar(fontsize = 10), show_quantiles = TRUE, column_order = NULL, column_names_side = "bottom", show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, cluster_columns = FALSE, clustering_distance_columns = "ks", clustering_method_columns = "complete", mc.cores = 1, cores = mc.cores, ...)densityHeatmap(data, density_param = list(na.rm = TRUE), col = rev(brewer.pal(11, "Spectral")), color_space = "LAB", ylab = deparse(substitute(data)), column_title = paste0("Density heatmap of ", deparse(substitute(data))), title = column_title, ylim = NULL, range = ylim, title_gp = gpar(fontsize = 14), ylab_gp = gpar(fontsize = 12), tick_label_gp = gpar(fontsize = 10), quantile_gp = gpar(fontsize = 10), show_quantiles = TRUE, column_order = NULL, column_names_side = "bottom", show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, cluster_columns = FALSE, clustering_distance_columns = "ks", clustering_method_columns = "complete", mc.cores = 1, cores = mc.cores, ...)
data |
A matrix or a list. If it is a matrix, density is calculated by columns. |
density_param |
Parameters send to |
col |
A vector of colors that density values are mapped to. |
color_space |
The color space in which colors are interpolated. Pass to |
ylab |
Label on y-axis. |
column_title |
Title of the heatmap. |
title |
Same as |
ylim |
Ranges on the y-axis. |
range |
Same as |
title_gp |
Graphic parameters for title. |
ylab_gp |
Graphic parameters for y-labels. |
tick_label_gp |
Graphic parameters for y-ticks. |
quantile_gp |
Graphic parameters for the quantiles. |
show_quantiles |
Whether show quantile lines. |
column_order |
Order of columns. |
column_names_side |
Pass to |
show_column_names |
Pass to |
column_names_max_height |
Pass to |
column_names_gp |
Pass to |
column_names_rot |
Pass to |
cluster_columns |
Whether cluster columns? |
clustering_distance_columns |
There is a specific distance method |
clustering_method_columns |
Pass to |
mc.cores |
Multiple cores for calculating ks distance. This argument will be removed in future versions. |
cores |
Multiple cores for calculating ks distance. |
... |
Pass to |
To visualize data distribution in a matrix or in a list, we normally use
boxplot or violinplot. We can also use colors to map the density values and
visualize distribution of values through a heatmap. It is useful if you have
huge number of columns in data to visualize.
The density matrix is generated with 500 rows ranging between the maximun and minimal values in all densities.
A Heatmap-class object. It can oly add other heatmaps/annotations vertically.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/other-high-level-plots.html#density-heatmap
matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt) ha = HeatmapAnnotation(points = anno_points(runif(10)), anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue"))) densityHeatmap(matrix, top_annotation = ha) densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] densityHeatmap(matrix) lt = list(rnorm(10), rnorm(10)) densityHeatmap(lt) ha = HeatmapAnnotation(points = anno_points(runif(10)), anno = rep(c("A", "B"), each = 5), col = list(anno = c("A" = "red", "B" = "blue"))) densityHeatmap(matrix, top_annotation = ha) densityHeatmap(matrix, top_annotation = ha) %v% Heatmap(matrix, height = unit(6, "cm"))
Dimension of the Heatmap
## S3 method for class 'Heatmap' dim(x)## S3 method for class 'Heatmap' dim(x)
x |
A |
# There is no example NULL# There is no example NULL
Calculate Pairwise Distance from a Matrix
dist2(x, pairwise_fun = function(x, y) sqrt(sum((x - y)^2)), ...)dist2(x, pairwise_fun = function(x, y) sqrt(sum((x - y)^2)), ...)
x |
A matrix or a list. If it is a matrix, the distance is calculated by rows. |
pairwise_fun |
A function which calculates distance between two vectors. |
... |
Pass to |
You can construct any type of distance measurements by defining a pair-wise distance function.
The function is implemented by two nested for loops, so the efficiency may not be so good.
A dist object.
Zuguang Gu <[email protected]>
lt = lapply(1:10, function(i) { sample(letters, sample(6:10, 1)) }) dist2(lt, function(x, y) { length(intersect(x, y))/length(union(x, y)) })lt = lapply(1:10, function(i) { sample(letters, sample(6:10, 1)) }) dist2(lt, function(x, y) { length(intersect(x, y))/length(union(x, y)) })
Draw legends for All Annotations
## S4 method for signature 'HeatmapList' draw_annotation_legend(object, legend_list = list(), ...)## S4 method for signature 'HeatmapList' draw_annotation_legend(object, legend_list = list(), ...)
object |
A |
legend_list |
A list of self-defined legends, should be wrapped into |
... |
Other arguments. |
We call the "annotation legends" as the secondary legends. For horizontal heamtap list, the legends are those from all top/bottom annotations, and for vertical heatmap list, the legends are those from all left/right annotations.
A viewport is created which contains annotation legends.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw Heatmap Annotations on the Heatmap
## S4 method for signature 'Heatmap' draw_annotation(object, which = c("top", "bottom", "left", "right"), k = 1, ...)## S4 method for signature 'Heatmap' draw_annotation(object, which = c("top", "bottom", "left", "right"), k = 1, ...)
object |
A |
which |
The position of the heamtap annotation. |
k |
Slice index. |
... |
Pass to |
A viewport is created which contains column/top annotations.
The function calls draw,HeatmapAnnotation-method to draw the annotations.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw Heatmap Dendrograms
## S4 method for signature 'Heatmap' draw_dend(object, which = c("row", "column"), k = 1, max_height = NULL, ...)## S4 method for signature 'Heatmap' draw_dend(object, which = c("row", "column"), k = 1, max_height = NULL, ...)
object |
A |
which |
Are the dendrograms put on the row or on the column of the heatmap? |
k |
Slice index. |
max_height |
maximal height of dendrogram. |
... |
Pass to |
A viewport is created which contains dendrograms.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw row names or column names
## S4 method for signature 'Heatmap' draw_dimnames(object, which = c("row", "column"), k = 1, ...)## S4 method for signature 'Heatmap' draw_dimnames(object, which = c("row", "column"), k = 1, ...)
object |
A |
which |
Are the names put on the row or on the column of the heatmap? |
k |
Slice index. |
... |
Pass to |
A viewport is created which contains row names or column names.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw Heatmap Body
## S4 method for signature 'Heatmap' draw_heatmap_body(object, kr = 1, kc = 1, ...)## S4 method for signature 'Heatmap' draw_heatmap_body(object, kr = 1, kc = 1, ...)
object |
A |
kr |
Row slice index. |
kc |
Column slice index. |
... |
Pass to |
A viewport is created which contains subset rows and columns of the heatmap.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw legends for All Heatmaps
## S4 method for signature 'HeatmapList' draw_heatmap_legend(object, legend_list = list(), ...)## S4 method for signature 'HeatmapList' draw_heatmap_legend(object, legend_list = list(), ...)
object |
A |
legend_list |
A list of self-defined legends, should be wrapped into |
... |
Other arguments. |
Actually we call the "heatmap legends" as the main legends.
For horizontal heatmap list, the legends are those from heamtap/row annotation/left/right annotation.
For vertical heatmap list, the legends are those from heamtap/column annotation/top/bottom annotation.
if merge_legends is true in draw,HeatmapList-method, then it contains all legends shown on the plot.
A viewport is created which contains heatmap legends.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw the List of Heatmaps
## S4 method for signature 'HeatmapList' draw_heatmap_list(object)## S4 method for signature 'HeatmapList' draw_heatmap_list(object)
object |
A |
It only draws the list of heatmaps without legends and titles.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Method dispatch page for draw_title.
draw_title can be dispatched on following classes:
draw_title,HeatmapList-method, HeatmapList-class class method
draw_title,Heatmap-method, Heatmap-class class method
# no example NULL# no example NULL
Draw Heatmap Title
## S4 method for signature 'Heatmap' draw_title(object, which = c("row", "column"), k = 1, ...)## S4 method for signature 'Heatmap' draw_title(object, which = c("row", "column"), k = 1, ...)
object |
A |
which |
Is title put on the row or on the column of the heatmap? |
k |
Slice index. |
... |
Pass to |
A viewport is created which contains heatmap title.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw Heatmap List Title
## S4 method for signature 'HeatmapList' draw_title(object, which = c("column", "row"))## S4 method for signature 'HeatmapList' draw_title(object, which = c("column", "row"))
object |
A |
which |
Is it a row title or a column title. |
A viewport is created which contains heatmap list title.
This function is only for internal use.
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw the AnnotationFunction Object
## S4 method for signature 'AnnotationFunction' draw(object, index, k = 1, n = 1, test = FALSE, ...)## S4 method for signature 'AnnotationFunction' draw(object, index, k = 1, n = 1, test = FALSE, ...)
object |
The |
index |
Index of observations. |
k |
Current slice index. |
n |
Total number of slices. |
test |
Is it in test mode? The value can be logical or a text which is plotted as the title of plot. |
... |
Pass to |
Normally it is called internally by the SingleAnnotation-class.
When test is set to TRUE, the annotation graphic is directly drawn,
which is generally for testing purpose.
# There is no example NULL# There is no example NULL
Method dispatch page for draw.
draw can be dispatched on following classes:
draw,HeatmapAnnotation-method, HeatmapAnnotation-class class method
draw,Legends-method, Legends-class class method
draw,SingleAnnotation-method, SingleAnnotation-class class method
draw,AnnotationFunction-method, AnnotationFunction-class class method
draw,Heatmap-method, Heatmap-class class method
draw,HeatmapList-method, HeatmapList-class class method
# no example NULL# no example NULL
Draw a Single Heatmap
## S4 method for signature 'Heatmap' draw(object, internal = FALSE, test = FALSE, ...)## S4 method for signature 'Heatmap' draw(object, internal = FALSE, test = FALSE, ...)
object |
A |
internal |
If |
test |
Only for testing. If it is |
... |
Pass to |
The function creates a HeatmapList-class object which only contains a single heatmap
and call draw,HeatmapList-method to make the final heatmap.
There are some arguments which control the some settings of the heatmap such as legends.
Please go to draw,HeatmapList-method for these arguments.
A HeatmapList-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw the Heatmap Annotations
## S4 method for signature 'HeatmapAnnotation' draw(object, index, k = 1, n = 1, ..., test = FALSE, anno_mark_param = list())## S4 method for signature 'HeatmapAnnotation' draw(object, index, k = 1, n = 1, ..., test = FALSE, anno_mark_param = list())
object |
A |
index |
A vector of indices. |
k |
The current slice index for the annotation if it is split. |
n |
Total number of slices. |
... |
Pass to |
test |
Is it in test mode? The value can be logical or a text which is plotted as the title of plot. |
anno_mark_param |
It contains specific parameters for drawing |
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw a list of heatmaps
## S4 method for signature 'HeatmapList' draw(object, newpage = TRUE, background = "white", row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 13), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 13), heatmap_legend_side = c("right", "left", "bottom", "top"), merge_legends = ht_opt$merge_legends, show_heatmap_legend = TRUE, heatmap_legend_list = list(), annotation_legend_side = c("right", "left", "bottom", "top"), show_annotation_legend = TRUE, annotation_legend_list = list(), align_heatmap_legend = NULL, align_annotation_legend = NULL, legend_grouping = c("adjusted", "original"), gap = unit(2, "mm"), ht_gap = gap, main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1], padding = GLOBAL_PADDING, adjust_annotation_extension = NULL, auto_adjust = TRUE, row_dend_side = c("original", "left", "right"), row_sub_title_side = c("original", "left", "right"), column_dend_side = c("original", "top", "bottom"), column_sub_title_side = c("original", "top", "bottom"), row_gap = NULL, cluster_rows = NULL, cluster_row_slices = NULL, clustering_distance_rows = NULL, clustering_method_rows = NULL, row_dend_width = NULL, show_row_dend = NULL, row_dend_reorder = NULL, row_dend_gp = NULL, row_order = NULL, km = NULL, split = NULL, row_km = km, row_km_repeats = NULL, row_split = split, height = NULL, heatmap_height = NULL, column_gap = NULL, cluster_columns = NULL, cluster_column_slices = NULL, clustering_distance_columns = NULL, clustering_method_columns = NULL, column_dend_width = NULL, show_column_dend = NULL, column_dend_reorder = NULL, column_dend_gp = NULL, column_order = NULL, column_km = NULL, column_km_repeats = NULL, column_split = NULL, width = NULL, heatmap_width = NULL, use_raster = NULL, raster_device = NULL, raster_quality = NULL, raster_device_param = NULL, raster_resize = NULL, post_fun = NULL, save_last = ht_opt$save_last, ### global setting heatmap_row_names_gp = NULL, heatmap_column_names_gp = NULL, heatmap_row_title_gp = NULL, heatmap_column_title_gp = NULL, legend_title_gp = NULL, legend_title_position = NULL, legend_labels_gp = NULL, legend_grid_height = NULL, legend_grid_width = NULL, legend_border = NULL, legend_gap = NULL, heatmap_border = NULL, annotation_border = NULL, fastcluster = NULL, simple_anno_size = NULL, show_parent_dend_line = NULL)## S4 method for signature 'HeatmapList' draw(object, newpage = TRUE, background = "white", row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 13), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 13), heatmap_legend_side = c("right", "left", "bottom", "top"), merge_legends = ht_opt$merge_legends, show_heatmap_legend = TRUE, heatmap_legend_list = list(), annotation_legend_side = c("right", "left", "bottom", "top"), show_annotation_legend = TRUE, annotation_legend_list = list(), align_heatmap_legend = NULL, align_annotation_legend = NULL, legend_grouping = c("adjusted", "original"), gap = unit(2, "mm"), ht_gap = gap, main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1], padding = GLOBAL_PADDING, adjust_annotation_extension = NULL, auto_adjust = TRUE, row_dend_side = c("original", "left", "right"), row_sub_title_side = c("original", "left", "right"), column_dend_side = c("original", "top", "bottom"), column_sub_title_side = c("original", "top", "bottom"), row_gap = NULL, cluster_rows = NULL, cluster_row_slices = NULL, clustering_distance_rows = NULL, clustering_method_rows = NULL, row_dend_width = NULL, show_row_dend = NULL, row_dend_reorder = NULL, row_dend_gp = NULL, row_order = NULL, km = NULL, split = NULL, row_km = km, row_km_repeats = NULL, row_split = split, height = NULL, heatmap_height = NULL, column_gap = NULL, cluster_columns = NULL, cluster_column_slices = NULL, clustering_distance_columns = NULL, clustering_method_columns = NULL, column_dend_width = NULL, show_column_dend = NULL, column_dend_reorder = NULL, column_dend_gp = NULL, column_order = NULL, column_km = NULL, column_km_repeats = NULL, column_split = NULL, width = NULL, heatmap_width = NULL, use_raster = NULL, raster_device = NULL, raster_quality = NULL, raster_device_param = NULL, raster_resize = NULL, post_fun = NULL, save_last = ht_opt$save_last, ### global setting heatmap_row_names_gp = NULL, heatmap_column_names_gp = NULL, heatmap_row_title_gp = NULL, heatmap_column_title_gp = NULL, legend_title_gp = NULL, legend_title_position = NULL, legend_labels_gp = NULL, legend_grid_height = NULL, legend_grid_width = NULL, legend_border = NULL, legend_gap = NULL, heatmap_border = NULL, annotation_border = NULL, fastcluster = NULL, simple_anno_size = NULL, show_parent_dend_line = NULL)
object |
a |
newpage |
whether create a new page for the graphics. If you want to arrange multiple plots in one page, I suggest to use |
background |
Background color of the whole plot. |
row_title |
title on the row. |
row_title_side |
will the title be put on the left or right of the heatmap. |
row_title_gp |
graphic parameters for drawing text. |
column_title |
title on the column. |
column_title_side |
will the title be put on the top or bottom of the heatmap. |
column_title_gp |
graphic parameters for drawing text. |
heatmap_legend_side |
side to put heatmap legend |
merge_legends |
merge heatmap legends and annotation legends to put into one column. |
show_heatmap_legend |
whether show all heatmap legends |
heatmap_legend_list |
use-defined legends which are put after the heatmap legends |
annotation_legend_side |
side of the annotation legends |
show_annotation_legend |
whether show annotation legends |
annotation_legend_list |
user-defined legends which are put after the annotation legends |
align_heatmap_legend |
How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is |
align_annotation_legend |
How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". |
legend_grouping |
How the legends are grouped. Values should be "adjusted" or "original". If it is set as "original", all annotation legends are grouped together. |
gap |
gap between heatmaps/annotations |
ht_gap |
same as |
main_heatmap |
index of main heatmap. The value can be a numeric index or the heatmap name |
padding |
padding of the whole plot. The value is a unit vector of length 4, which corresponds to bottom, left, top and right. |
adjust_annotation_extension |
whether take annotation name into account when calculating positions of graphic elements. |
auto_adjust |
whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps. |
row_dend_side |
side of the dendrogram from the main heatmap |
row_sub_title_side |
side of the row title from the main heatmap |
column_dend_side |
side of the dendrogram from the main heatmap |
column_sub_title_side |
side of the column title from the main heatmap |
row_gap |
this modifies |
cluster_rows |
this modifies |
cluster_row_slices |
this modifies |
clustering_distance_rows |
this modifies |
clustering_method_rows |
this modifies |
row_dend_width |
this modifies |
show_row_dend |
this modifies |
row_dend_reorder |
this modifies |
row_dend_gp |
this modifies |
row_order |
this modifies |
km |
= this modifies |
split |
this modifies |
row_km |
this modifies |
row_km_repeats |
this modifies |
row_split |
this modifies |
height |
this modifies |
heatmap_height |
this modifies |
column_gap |
this modifies |
cluster_columns |
this modifies |
cluster_column_slices |
this modifies |
clustering_distance_columns |
this modifies |
clustering_method_columns |
this modifies |
column_dend_width |
this modifies |
show_column_dend |
this modifies |
column_dend_reorder |
this modifies |
column_dend_gp |
this modifies |
column_order |
this modifies |
column_km |
this modifies |
column_km_repeats |
this modifies |
column_split |
this modifies |
width |
this modifies |
heatmap_width |
this modifies |
use_raster |
this modifies |
raster_device |
this modifies |
raster_quality |
this modifies |
raster_device_param |
this modifies |
raster_resize |
this modifies |
post_fun |
A self-defined function will be executed after all the heatmaps are drawn. |
save_last |
Whether to save the last plot? |
heatmap_row_names_gp |
this set the value in |
heatmap_column_names_gp |
this set the value in |
heatmap_row_title_gp |
this set the value in |
heatmap_column_title_gp |
this set the value in |
legend_title_gp |
this set the value in |
legend_title_position |
this set the value in |
legend_labels_gp |
this set the value in |
legend_grid_height |
this set the value in |
legend_grid_width |
this set the value in |
legend_border |
this set the value in |
legend_gap |
Gap between legends. The value should be a vector of two units. One for gaps between vertical legends and one for the horizontal legends. If only one single unit is specified, the same gap set for the vertical and horizontal legends. |
heatmap_border |
this set the value in |
annotation_border |
this set the value in |
fastcluster |
this set the value in |
simple_anno_size |
this set the value in |
show_parent_dend_line |
this set the value in |
The function first calls make_layout,HeatmapList-method to calculate
the layout of the heatmap list and the layout of every single heatmap,
then makes the plot by re-calling the graphic functions which are already recorded
in the layout.
This function returns a HeatmapList-class object for which the layout has been created.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html
# There is no example NULL# There is no example NULL
Draw the Legends
## S4 method for signature 'Legends' draw(object, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", test = FALSE)## S4 method for signature 'Legends' draw(object, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", test = FALSE)
object |
The |
x |
The x position of the legends, measured in current viewport. |
y |
The y position of the legends, measured in current viewport. |
just |
Justification of the legends. |
test |
Only used for testing. |
In the legend grob, there should always be a viewport attached which is like a wrapper of
all the graphic elements in a legend.
If in the object, there is already a viewport attached, it will modify the x, y
and valid.just of the viewport. If there is not viewport attached, a viewport
with specified x, y and valid.just is created and attached.
You can also directly use grid.draw to draw the legend object, but you can
only control the position of the legends by first creating a parent viewport and adjusting
the position of the parent viewport.
lgd = Legend(at = 1:4, title = "foo") draw(lgd, x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom")) # and a similar version of grid.draw pushViewport(viewport(x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom"))) grid.draw(lgd) popViewport()lgd = Legend(at = 1:4, title = "foo") draw(lgd, x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom")) # and a similar version of grid.draw pushViewport(viewport(x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom"))) grid.draw(lgd) popViewport()
Draw the Single Annotation
## S4 method for signature 'SingleAnnotation' draw(object, index, k = 1, n = 1, test = FALSE, anno_mark_param = list())## S4 method for signature 'SingleAnnotation' draw(object, index, k = 1, n = 1, test = FALSE, anno_mark_param = list())
object |
A |
index |
A vector of indices. |
k |
The index of the slice. |
n |
Total number of slices. |
test |
Is it in test mode? The value can be logical or a text which is plotted as the title of plot. |
anno_mark_param |
It contains specific parameters for drawing |
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Extract Elements in a Combination set
extract_comb(m, comb_name)extract_comb(m, comb_name)
m |
A combination matrix returned by |
comb_name |
The valid combination set name should be from |
It returns the combination set.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) extract_comb(m, "110")set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) extract_comb(m, "110")
Visualize Frequency Distribution by Heatmap
frequencyHeatmap(data, breaks = "Sturges", stat = c("count", "density", "proportion"), col = brewer.pal(9, "Blues"), color_space = "LAB", ylab = deparse(substitute(data)), column_title = paste0("Frequency heatmap of ", deparse(substitute(data))), title = column_title, ylim = NULL, range = ylim, title_gp = gpar(fontsize = 14), ylab_gp = gpar(fontsize = 12), tick_label_gp = gpar(fontsize = 10), column_order = NULL, column_names_side = "bottom", show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, cluster_columns = FALSE, use_3d = FALSE, ...)frequencyHeatmap(data, breaks = "Sturges", stat = c("count", "density", "proportion"), col = brewer.pal(9, "Blues"), color_space = "LAB", ylab = deparse(substitute(data)), column_title = paste0("Frequency heatmap of ", deparse(substitute(data))), title = column_title, ylim = NULL, range = ylim, title_gp = gpar(fontsize = 14), ylab_gp = gpar(fontsize = 12), tick_label_gp = gpar(fontsize = 10), column_order = NULL, column_names_side = "bottom", show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, cluster_columns = FALSE, use_3d = FALSE, ...)
data |
A matrix or a list. If it is a matrix, density is calculated by columns. |
breaks |
Pass to |
stat |
Statistic to use. |
col |
A vector of colors that density values are mapped to. |
color_space |
The color space in which colors are interpolated. Pass to |
ylab |
Label on y-axis. |
column_title |
Title of the heatmap. |
title |
Same as |
ylim |
Ranges on the y-axis. |
range |
Same as |
title_gp |
Graphic parameters for title. |
ylab_gp |
Graphic parameters for y-labels. |
tick_label_gp |
Graphic parameters for y-ticks. |
column_order |
Order of columns. |
column_names_side |
Pass to |
show_column_names |
Pass to |
column_names_max_height |
Pass to |
column_names_gp |
Pass to |
column_names_rot |
Pass to |
cluster_columns |
Whether cluster columns? |
use_3d |
Whether to visualize the frequencies as a 3D heatmap with |
... |
A Heatmap-class object. It can oly add other heatmaps/annotations vertically.
Zuguang Gu <[email protected]>
matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] frequencyHeatmap(matrix) frequencyHeatmap(matrix, use_3d = TRUE)matrix = matrix(rnorm(100), 10); colnames(matrix) = letters[1:10] frequencyHeatmap(matrix) frequencyHeatmap(matrix, use_3d = TRUE)
Full set of code of combination sets
full_comb_code(n, complement = FALSE)full_comb_code(n, complement = FALSE)
n |
Number of sets |
complement |
Whether include the code for complement set? |
full_comb_code(2) full_comb_code(3) full_comb_code(4) full_comb_code(4, TRUE)full_comb_code(2) full_comb_code(3) full_comb_code(4) full_comb_code(4, TRUE)
Get a List of ColorMapping objects
## S4 method for signature 'HeatmapAnnotation' get_color_mapping_list(object)## S4 method for signature 'HeatmapAnnotation' get_color_mapping_list(object)
object |
A |
Color mappings for visible simple annotations are only returned.
This function is only for internal use.
A list of ColorMapping-class objects or an empty list.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Get a List of Annotation Legend Parameters
## S4 method for signature 'HeatmapAnnotation' get_legend_param_list(object)## S4 method for signature 'HeatmapAnnotation' get_legend_param_list(object)
object |
A |
The annotation legend parameters for visible simple annotations are only returned.
This function is only for internal use.
A list.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Convert XY in a Parent Viewport
getXY_in_parent_vp(u, vp_name = "ROOT")getXY_in_parent_vp(u, vp_name = "ROOT")
u |
A list of two units which correspond to x and y. |
vp_name |
The name of the parent viewport. |
It converts a coordinate measured in current viewport to the coordinate in a parent viewport.
In the conversion, all units are recalculated as absolute units, so if you change the size of the interactive graphic window, you need to rerun the function.
A list of two units.
grid.newpage() pushViewport(viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.5, just = c("left", "bottom"))) grid.rect() grid.points(x = unit(2, "cm"), y = unit(2, "cm"), pch = 1) u = list(x = unit(2, "cm"), y = unit(2, "cm")) u2 = getXY_in_parent_vp(u) popViewport() grid.rect(gp = gpar(col = "red")) grid.points(x = u2$x, u2$y, pch = 2)grid.newpage() pushViewport(viewport(x = 0.5, y = 0.5, width = 0.5, height = 0.5, just = c("left", "bottom"))) grid.rect() grid.points(x = unit(2, "cm"), y = unit(2, "cm"), pch = 1) u = list(x = unit(2, "cm"), y = unit(2, "cm")) u2 = getXY_in_parent_vp(u) popViewport() grid.rect(gp = gpar(col = "red")) grid.points(x = u2$x, u2$y, pch = 2)
Draw Annotation Axis
grid.annotation_axis(at = NULL, labels = at, labels_rot = 0, gp = gpar(), side = "left", facing = "outside", direction = "normal")grid.annotation_axis(at = NULL, labels = at, labels_rot = 0, gp = gpar(), side = "left", facing = "outside", direction = "normal")
at |
Break values. If it is not specified, it is inferred from data scale in current viewport. |
labels |
Corresponding labels. |
labels_rot |
Rotations of labels. |
gp |
Graphic parameters. |
side |
side of the axis of the annotation viewport. |
facing |
Facing of the axis. |
direction |
direction of the axis. Value should be "normal" or "reverse". |
It uses annotation_axis_grob to construct the grob object, then use grid.draw
to draw the axis.
# See examples in `annotation_axis_grob` NULL# See examples in `annotation_axis_grob` NULL
Draw a Single Boxplot
grid.boxplot(value, pos, outline = TRUE, box_width = 0.6, pch = 1, size = unit(2, "mm"), gp = gpar(fill = "#CCCCCC"), direction = c("vertical", "horizontal"))grid.boxplot(value, pos, outline = TRUE, box_width = 0.6, pch = 1, size = unit(2, "mm"), gp = gpar(fill = "#CCCCCC"), direction = c("vertical", "horizontal"))
value |
A vector of numeric values. |
pos |
Position of the boxplot. |
outline |
Whether draw outlines? |
box_width |
width of the box. |
pch |
Point type. |
size |
Point size. |
gp |
Graphic parameters. |
direction |
Whether the box is vertical or horizontal. |
All the values are measured with native coordinate.
lt = list(rnorm(100), rnorm(100)) grid.newpage() pushViewport(viewport(xscale = c(0.5, 2.5), yscale = range(lt))) grid.boxplot(lt[[1]], pos = 1, gp = gpar(fill = "red")) grid.boxplot(lt[[2]], pos = 2, gp = gpar(fill = "green")) popViewport()lt = list(rnorm(100), rnorm(100)) grid.newpage() pushViewport(viewport(xscale = c(0.5, 2.5), yscale = range(lt))) grid.boxplot(lt[[1]], pos = 1, gp = gpar(fill = "red")) grid.boxplot(lt[[2]], pos = 2, gp = gpar(fill = "green")) popViewport()
Draw the Dendrogram
grid.dendrogram(dend, ..., test = FALSE)grid.dendrogram(dend, ..., test = FALSE)
dend |
A |
... |
Pass to |
test |
Is it in test mode? If it is in test mode, a viewport is created by calculating proper xlim and ylim. |
grid.dendrogram supports drawing dendrograms with self-defind leaf positions. The positions
of leaves can be defined by adjust_dend_by_x. Also the dendrogram can be customized by setting
the edgePar attribute for each node (basically for controlling the style of segments), e.g.
by color_branches.
To draw the dendrogram, a viewport should be firstly created. dend_xy can be used to get the
positions of leaves and height of the dendrogram.
m = matrix(rnorm(100), 10) dend = as.dendrogram(hclust(dist(m))) grid.newpage() pushViewport(viewport(xscale = c(0, 10.5), yscale = c(0, dend_heights(dend)), width = 0.9, height = 0.9)) grid.dendrogram(dend) popViewport() grid.dendrogram(dend, test = TRUE) require(dendextend) dend = color_branches(dend, k = 2) dend = adjust_dend_by_x(dend, unit(sort(runif(10)*10), "cm")) grid.dendrogram(dend, test = TRUE)m = matrix(rnorm(100), 10) dend = as.dendrogram(hclust(dist(m))) grid.newpage() pushViewport(viewport(xscale = c(0, 10.5), yscale = c(0, dend_heights(dend)), width = 0.9, height = 0.9)) grid.dendrogram(dend) popViewport() grid.dendrogram(dend, test = TRUE) require(dendextend) dend = color_branches(dend, k = 2) dend = adjust_dend_by_x(dend, unit(sort(runif(10)*10), "cm")) grid.dendrogram(dend, test = TRUE)
Draw the Legends
## S3 method for class 'Legends' grid.draw(x, recording = TRUE)## S3 method for class 'Legends' grid.draw(x, recording = TRUE)
x |
The |
recording |
Pass to |
This function is actually an S3 method of the Legends class for the grid.draw
general method. It applies grid.draw on the grob slot of the object.
lgd = Legend(at = 1:4, title = "foo") pushViewport(viewport(x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom"))) grid.draw(lgd) popViewport()lgd = Legend(at = 1:4, title = "foo") pushViewport(viewport(x = unit(0, "npc"), y = unit(0, "npc"), just = c("left", "bottom"))) grid.draw(lgd) popViewport()
Draw multiple texts in a box
grid.textbox(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...)grid.textbox(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...)
text |
A vector of texts. The value can be single words or phrases/sentenses. |
x |
X position. |
y |
Y position. |
gp |
Graphics parameters of texts. |
... |
Pass to |
All details can be found in the help page of textbox_grob.
# There is no example NULL# There is no example NULL
Mark the text for the rendering by gridtext package
gt_render(x, ...)gt_render(x, ...)
x |
Text labels. The value can be a vector. |
... |
Other parameters passed to |
Text marked by gt_render will be rendered by richtext_grob function.
if(requireNamespace("gridtext")) { mat = matrix(rnorm(100), 10) rownames(mat) = letters[1:10] ht = Heatmap(mat, column_title = gt_render("Some <span style='color:blue'>blue text **in bold.**</span><br>And *italics text.*<br>And some <span style='font-size:18pt; color:black'>large</span> text.", r = unit(2, "pt"), padding = unit(c(2, 2, 2, 2), "pt")), column_title_gp = gpar(box_fill = "orange"), row_labels = gt_render(letters[1:10], padding = unit(c(2, 10, 2, 10), "pt")), row_names_gp = gpar(box_col = "red"), row_km = 2, row_title = gt_render(c("title1", "title2")), row_title_gp = gpar(box_fill = "yellow"), heatmap_legend_param = list( title = gt_render("<span style='color:orange'>**Legend title**</span>"), title_gp = gpar(box_fill = "grey"), at = c(-3, 0, 3), labels = gt_render(c("*negative* three", "zero", "*positive* three")) )) ht = rowAnnotation( foo = anno_text(gt_render(sapply(LETTERS[1:10], strrep, 10), align_widths = TRUE), gp = gpar(box_col = "blue", box_lwd = 2), just = "right", location = unit(1, "npc") )) + ht draw(ht) }if(requireNamespace("gridtext")) { mat = matrix(rnorm(100), 10) rownames(mat) = letters[1:10] ht = Heatmap(mat, column_title = gt_render("Some <span style='color:blue'>blue text **in bold.**</span><br>And *italics text.*<br>And some <span style='font-size:18pt; color:black'>large</span> text.", r = unit(2, "pt"), padding = unit(c(2, 2, 2, 2), "pt")), column_title_gp = gpar(box_fill = "orange"), row_labels = gt_render(letters[1:10], padding = unit(c(2, 10, 2, 10), "pt")), row_names_gp = gpar(box_col = "red"), row_km = 2, row_title = gt_render(c("title1", "title2")), row_title_gp = gpar(box_fill = "yellow"), heatmap_legend_param = list( title = gt_render("<span style='color:orange'>**Legend title**</span>"), title_gp = gpar(box_fill = "grey"), at = c(-3, 0, 3), labels = gt_render(c("*negative* three", "zero", "*positive* three")) )) ht = rowAnnotation( foo = anno_text(gt_render(sapply(LETTERS[1:10], strrep, 10), align_widths = TRUE), gp = gpar(box_col = "blue", box_lwd = 2), just = "right", location = unit(1, "npc") )) + ht draw(ht) }
Constructor method for Heatmap class
Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB", rect_gp = gpar(col = NA), border = NA, border_gp = gpar(col = "black"), cell_fun = NULL, layer_fun = NULL, jitter = FALSE, row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 13.2), row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 13.2), column_title_rot = 0, cluster_rows = TRUE, cluster_row_slices = TRUE, clustering_distance_rows = "euclidean", clustering_method_rows = "complete", row_dend_side = c("left", "right"), row_dend_width = unit(10, "mm"), show_row_dend = TRUE, row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows), row_dend_gp = gpar(), cluster_columns = TRUE, cluster_column_slices = TRUE, clustering_distance_columns = "euclidean", clustering_method_columns = "complete", column_dend_side = c("top", "bottom"), column_dend_height = unit(10, "mm"), show_column_dend = TRUE, column_dend_gp = gpar(), column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns), row_order = NULL, column_order = NULL, row_labels = rownames(matrix), row_names_side = c("right", "left"), show_row_names = TRUE, row_names_max_width = unit(6, "cm"), row_names_gp = gpar(fontsize = 12), row_names_rot = 0, row_names_centered = FALSE, column_labels = colnames(matrix), column_names_side = c("bottom", "top"), show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, column_names_centered = FALSE, top_annotation = NULL, bottom_annotation = NULL, left_annotation = NULL, right_annotation = NULL, km = 1, split = NULL, row_km = km, row_km_repeats = 1, row_split = split, column_km = 1, column_km_repeats = 1, column_split = NULL, gap = unit(1, "mm"), row_gap = unit(1, "mm"), column_gap = unit(1, "mm"), show_parent_dend_line = ht_opt$show_parent_dend_line, heatmap_width = unit(1, "npc"), width = NULL, heatmap_height = unit(1, "npc"), height = NULL, show_heatmap_legend = TRUE, heatmap_legend_param = list(title = name), use_raster = NULL, raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF", "agg_png"), raster_quality = 1, raster_device_param = list(), raster_resize_mat = FALSE, raster_by_magick = requireNamespace("magick", quietly = TRUE), raster_magick_filter = NULL, post_fun = NULL)Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB", rect_gp = gpar(col = NA), border = NA, border_gp = gpar(col = "black"), cell_fun = NULL, layer_fun = NULL, jitter = FALSE, row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 13.2), row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 13.2), column_title_rot = 0, cluster_rows = TRUE, cluster_row_slices = TRUE, clustering_distance_rows = "euclidean", clustering_method_rows = "complete", row_dend_side = c("left", "right"), row_dend_width = unit(10, "mm"), show_row_dend = TRUE, row_dend_reorder = is.logical(cluster_rows) || is.function(cluster_rows), row_dend_gp = gpar(), cluster_columns = TRUE, cluster_column_slices = TRUE, clustering_distance_columns = "euclidean", clustering_method_columns = "complete", column_dend_side = c("top", "bottom"), column_dend_height = unit(10, "mm"), show_column_dend = TRUE, column_dend_gp = gpar(), column_dend_reorder = is.logical(cluster_columns) || is.function(cluster_columns), row_order = NULL, column_order = NULL, row_labels = rownames(matrix), row_names_side = c("right", "left"), show_row_names = TRUE, row_names_max_width = unit(6, "cm"), row_names_gp = gpar(fontsize = 12), row_names_rot = 0, row_names_centered = FALSE, column_labels = colnames(matrix), column_names_side = c("bottom", "top"), show_column_names = TRUE, column_names_max_height = unit(6, "cm"), column_names_gp = gpar(fontsize = 12), column_names_rot = 90, column_names_centered = FALSE, top_annotation = NULL, bottom_annotation = NULL, left_annotation = NULL, right_annotation = NULL, km = 1, split = NULL, row_km = km, row_km_repeats = 1, row_split = split, column_km = 1, column_km_repeats = 1, column_split = NULL, gap = unit(1, "mm"), row_gap = unit(1, "mm"), column_gap = unit(1, "mm"), show_parent_dend_line = ht_opt$show_parent_dend_line, heatmap_width = unit(1, "npc"), width = NULL, heatmap_height = unit(1, "npc"), height = NULL, show_heatmap_legend = TRUE, heatmap_legend_param = list(title = name), use_raster = NULL, raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF", "agg_png"), raster_quality = 1, raster_device_param = list(), raster_resize_mat = FALSE, raster_by_magick = requireNamespace("magick", quietly = TRUE), raster_magick_filter = NULL, post_fun = NULL)
matrix |
A matrix. Either numeric or character. If it is a simple vector, it will be converted to a one-column matrix. |
col |
A vector of colors if the color mapping is discrete or a color mapping function if the matrix is continuous numbers (should be generated by |
name |
Name of the heatmap. By default the heatmap name is used as the title of the heatmap legend. |
na_col |
Color for |
rect_gp |
Graphic parameters for drawing rectangles (for heatmap body). The value should be specified by |
color_space |
The color space in which colors are interpolated. Only used if |
border |
Whether draw border. The value can be logical or a string of color. |
border_gp |
Graphic parameters for the borders. If you want to set different parameters for different heatmap slices, please consider to use |
cell_fun |
Self-defined function to add graphics on each cell. Seven parameters will be passed into this function: |
layer_fun |
Similar as |
jitter |
Random shifts added to the matrix. The value can be logical or a single numeric value. It it is |
row_title |
Title on the row. |
row_title_side |
Will the title be put on the left or right of the heatmap? |
row_title_gp |
Graphic parameters for row title. |
row_title_rot |
Rotation of row title. |
column_title |
Title on the column. |
column_title_side |
Will the title be put on the top or bottom of the heatmap? |
column_title_gp |
Graphic parameters for column title. |
column_title_rot |
Rotation of column titles. |
cluster_rows |
If the value is a logical, it controls whether to make cluster on rows. The value can also be a |
cluster_row_slices |
If rows are split into slices, whether perform clustering on the slice means? |
clustering_distance_rows |
It can be a pre-defined character which is in ("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman", "kendall"). It can also be a function. If the function has one argument, the input argument should be a matrix and the returned value should be a |
clustering_method_rows |
Method to perform hierarchical clustering, pass to |
row_dend_side |
Should the row dendrogram be put on the left or right of the heatmap? |
row_dend_width |
Width of the row dendrogram, should be a |
show_row_dend |
Whether show row dendrogram? |
row_dend_gp |
Graphic parameters for the dendrogram segments. If users already provide a |
row_dend_reorder |
Apply reordering on row dendrograms. The value can be a logical value or a vector which contains weight which is used to reorder rows. The reordering is applied by |
cluster_columns |
Whether make cluster on columns? Same settings as |
cluster_column_slices |
If columns are split into slices, whether perform clustering on the slice means? |
clustering_distance_columns |
Same setting as |
clustering_method_columns |
Method to perform hierarchical clustering, pass to |
column_dend_side |
Should the column dendrogram be put on the top or bottom of the heatmap? |
column_dend_height |
height of the column cluster, should be a |
show_column_dend |
Whether show column dendrogram? |
column_dend_gp |
Graphic parameters for dendrogram segments. Same settings as |
column_dend_reorder |
Apply reordering on column dendrograms. Same settings as |
row_order |
Order of rows. Manually setting row order turns off clustering. |
column_order |
Order of column. |
row_labels |
Optional row labels which are put as row names in the heatmap. |
row_names_side |
Should the row names be put on the left or right of the heatmap? |
show_row_names |
Whether show row names. |
row_names_max_width |
Maximum width of row names viewport. |
row_names_gp |
Graphic parameters for row names. |
row_names_rot |
Rotation of row names. |
row_names_centered |
Should row names put centered? |
column_labels |
Optional column labels which are put as column names in the heatmap. |
column_names_side |
Should the column names be put on the top or bottom of the heatmap? |
column_names_max_height |
Maximum height of column names viewport. |
show_column_names |
Whether show column names. |
column_names_gp |
Graphic parameters for drawing text. |
column_names_rot |
Rotation of column names. |
column_names_centered |
Should column names put centered? |
top_annotation |
A |
bottom_annotation |
A |
left_annotation |
It should be specified by |
right_annotation |
it should be specified by |
km |
Apply k-means clustering on rows. If the value is larger than 1, the heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical clustering is still applied with parameters above. |
split |
A vector or a data frame by which the rows are split. But if |
row_km |
Same as |
row_km_repeats |
Number of k-means runs to get a consensus k-means clustering. Note if |
row_split |
Same as |
column_km |
K-means clustering on columns. |
column_km_repeats |
Number of k-means runs to get a consensus k-means clustering. Similar as |
column_split |
Split on columns. For heatmap splitting, please refer to https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-split . |
gap |
Gap between row slices if the heatmap is split by rows. The value should be a |
row_gap |
Same as |
column_gap |
Gap between column slices. |
show_parent_dend_line |
When heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms? |
width |
Width of the heatmap body. |
height |
Height of the heatmap body. |
heatmap_width |
Width of the whole heatmap (including heatmap components) |
heatmap_height |
Height of the whole heatmap (including heatmap components). Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#size-of-the-heatmap . |
show_heatmap_legend |
Whether show heatmap legend? |
heatmap_legend_param |
A list contains parameters for the heatmap legends. See |
use_raster |
Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. If number of rows or columns is more than 2000, it is by default turned on. Note if |
raster_device |
Graphic device which is used to generate the raster image. |
raster_quality |
A value larger than 1. |
raster_device_param |
A list of further parameters for the selected graphic device. For raster image support, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image . |
raster_resize_mat |
Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is |
raster_by_magick |
Whether to use |
raster_magick_filter |
Pass to |
post_fun |
A function which will be executed after the heatmap list is drawn. |
The initialization function only applies parameter checking and fill values to the slots with some validation.
Following methods can be applied to the Heatmap-class object:
show,Heatmap-method: draw a single heatmap with default parameters
draw,Heatmap-method: draw a single heatmap.
+ or %v% append heatmaps and annotations to a list of heatmaps.
The constructor function pretends to be a high-level graphic function because the show method
of the Heatmap-class object actually plots the graphics.
A Heatmap-class object.
Zuguang Gu <[email protected]>
https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html
# There is no example NULL# There is no example NULL
Size of the Heatmap Legends
## S4 method for signature 'HeatmapList' heatmap_legend_size(object, legend_list = list(), ...)## S4 method for signature 'HeatmapList' heatmap_legend_size(object, legend_list = list(), ...)
object |
A |
legend_list |
A list of self-defined legend, should be wrapped into |
... |
Other arguments. |
Internally, all heatmap legends are packed by packLegend as a single grob object.
This function is only for internal use.
A unit object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Class for a Single Heatmap
The Heatmap-class is not responsible for heatmap legend and annotation legends. The draw,Heatmap-method method
constructs a HeatmapList-class object which only contains one single heatmap
and call draw,HeatmapList-method to make the complete heatmap.
The Heatmap-class provides following methods:
Heatmap: constructor method.
draw,Heatmap-method: draw a single heatmap.
add_heatmap,Heatmap-method append heatmaps and annotations to a list of heatmaps.
row_order,HeatmapList-method: get order of rows
column_order,HeatmapList-method: get order of columns
row_dend,HeatmapList-method: get row dendrograms
column_dend,HeatmapList-method: get column dendrograms
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
3D Heatmap
Heatmap3D(matrix, ..., bar_rel_width = 0.6, bar_rel_height = 0.6, bar_max_length = unit(1, "cm"), bar_angle = 60, row_names_side = "left", show_row_dend = FALSE, show_column_dend = FALSE)Heatmap3D(matrix, ..., bar_rel_width = 0.6, bar_rel_height = 0.6, bar_max_length = unit(1, "cm"), bar_angle = 60, row_names_side = "left", show_row_dend = FALSE, show_column_dend = FALSE)
matrix |
The input matrix. Values should be non-negative. |
... |
All pass to |
bar_rel_width |
A factor between 0 and 1. |
bar_rel_height |
A factor between 0 and 1. |
bar_max_length |
Maximal length of bars. Value should be in absolute unit. |
bar_angle |
Angle for the projection. |
row_names_side |
Row names are by default put on the left side of the heatmap. |
show_row_dend |
By default the dendrogram is not drawn. |
show_column_dend |
By default the dendrogram is not drawn. |
For large matrices, the plotting might be slow.
m = matrix(sample(100, 36), 6) Heatmap3D(m)m = matrix(sample(100, 36), 6) Heatmap3D(m)
Constructor Method for HeatmapAnnotation class
HeatmapAnnotation(..., df = NULL, name, col, na_col = "grey", annotation_legend_param = list(), show_legend = TRUE, which = c("column", "row"), gp = gpar(col = NA), border = FALSE, gap = unit(1, "points"), show_annotation_name = TRUE, annotation_label = NULL, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = ifelse(which == "column", "right", "bottom"), annotation_name_rot = NULL, annotation_name_align = FALSE, annotation_height = NULL, annotation_width = NULL, height = NULL, width = NULL, simple_anno_size = ht_opt$simple_anno_size, simple_anno_size_adjust = FALSE)HeatmapAnnotation(..., df = NULL, name, col, na_col = "grey", annotation_legend_param = list(), show_legend = TRUE, which = c("column", "row"), gp = gpar(col = NA), border = FALSE, gap = unit(1, "points"), show_annotation_name = TRUE, annotation_label = NULL, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = ifelse(which == "column", "right", "bottom"), annotation_name_rot = NULL, annotation_name_align = FALSE, annotation_height = NULL, annotation_width = NULL, height = NULL, width = NULL, simple_anno_size = ht_opt$simple_anno_size, simple_anno_size_adjust = FALSE)
... |
Name-value pairs where the names correspond to annotation names and values can be a vector, a matrix and an annotation function. Each pair is sent to |
df |
A data frame. Each column will be treated as a simple annotation. The data frame must have column names. |
name |
Name of the heatmap annotation, optional. |
col |
A list of colors which contain color mapping to |
na_col |
Color for |
annotation_legend_param |
A list which contains parameters for annotation legends. See |
show_legend |
Whether show annotation legends. The value can be one single value or a vector. |
which |
Are these row annotations or column annotations? |
gp |
Graphic parameters for simple annotations (with |
border |
border of single annotations. |
gap |
Gap between annotations. It can be a single value or a vector of |
show_annotation_name |
Whether show annotation names? For column annotation, annotation names are drawn either on the left or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector. |
annotation_label |
Labels for the annotations. By default it is the same as individual annotation names. |
annotation_name_gp |
Graphic parameters for anntation names. Graphic paramters can be vectors. |
annotation_name_offset |
Offset to the annotation names, a |
annotation_name_side |
Side of the annotation names. |
annotation_name_rot |
Rotation of the annotation names. The value can be a vector. |
annotation_name_align |
Whether to align the annotation names. |
annotation_height |
Height of each annotation if annotations are column annotations. |
annotation_width |
Width of each annotation if annotations are row annotations. |
height |
Height of the whole column annotations. |
width |
Width of the whole heatmap annotations. |
simple_anno_size |
Size of the simple annotation. |
simple_anno_size_adjust |
Whether also adjust the size of simple annotations when adjusting the whole heatmap annotation. |
For arguments show_legend, border, annotation_name_offset, annotation_name_side, annotation_name_rot,
show_annotation_name, they can be set as named vectors to modify values for some of the annotations,
e.g. assuming you have an annotation with name foo, you can specify border = c(foo = TRUE) in HeatmapAnnotation.
There are three ways to specify heatmap annotations:
1. If the annotation is simply a vector or a matrix, it can be specified like HeatmapAnnotation(foo = 1:10).
2. If the annotations are already stored as a data frame, it can be specified like HeatmapAnnotation(df = df).
3. For complex annotations, users can use the pre-defined annotation functions such as anno_points: HeatmapAnnotation(foo = anno_points(1:10)).
For more details and examples, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html.
A HeatmapAnnotation-class object.
Zuguang Gu <[email protected]>
There are two helper functions: rowAnnotation and columnAnnotation.
# There is no example NULL# There is no example NULL
Class for Heatmap Annotations
A complex heatmap contains a list of annotations which are represented as graphics
placed on rows and columns. The HeatmapAnnotation-class contains a list of single annotations which are
represented as a list of SingleAnnotation-class objects.
The HeatmapAnnotation-class provides following methods:
HeatmapAnnotation: constructor method.
draw,HeatmapAnnotation-method: draw the annotations.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Constructor method for HeatmapList class
HeatmapList(...)HeatmapList(...)
... |
arguments |
There is no public constructor method for the HeatmapList-class.
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Class for a list of heatmaps
A heatmap list is defined as a list of heatmaps and annotations.
The HeatmapList-class provides following methods:
draw,HeatmapList-method: draw the list of heatmaps and row annotations.
add_heatmap,HeatmapList-method: add heatmaps to the list of heatmaps.
row_order,HeatmapList-method: get order of rows
column_order,HeatmapList-method: get order of columns
row_dend,HeatmapList-method: get row dendrograms
column_dend,HeatmapList-method: get column dendrograms
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Height of the AnnotationFunction Object
## S3 method for class 'AnnotationFunction' height(x, ...)## S3 method for class 'AnnotationFunction' height(x, ...)
x |
The |
... |
Other arguments. |
Internally used.
anno = anno_points(1:10) ComplexHeatmap:::height(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::height(anno)anno = anno_points(1:10) ComplexHeatmap:::height(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::height(anno)
Height of the Heatmap
## S3 method for class 'Heatmap' height(x, ...)## S3 method for class 'Heatmap' height(x, ...)
x |
The |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Height of the HeatmapAnnotation Object
## S3 method for class 'HeatmapAnnotation' height(x, ...)## S3 method for class 'HeatmapAnnotation' height(x, ...)
x |
The |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Height of the Heatmap List
## S3 method for class 'HeatmapList' height(x, ...)## S3 method for class 'HeatmapList' height(x, ...)
x |
The |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Height of the Legends
## S3 method for class 'Legends' height(x, ...)## S3 method for class 'Legends' height(x, ...)
x |
The |
... |
Other arguments. |
The returned unit x is always in mm.
lgd = Legend(labels = 1:10, title = "foo", legend_gp = gpar(fill = "red")) ComplexHeatmap:::height(lgd)lgd = Legend(labels = 1:10, title = "foo", legend_gp = gpar(fill = "red")) ComplexHeatmap:::height(lgd)
Height of the SingleAnnotation object
## S3 method for class 'SingleAnnotation' height(x, ...)## S3 method for class 'SingleAnnotation' height(x, ...)
x |
The |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Height to the AnnotationFunction Object
## S3 replacement method for class 'AnnotationFunction' height(x, ...) <- value## S3 replacement method for class 'AnnotationFunction' height(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Height to the HeatmapAnnotation Object
## S3 replacement method for class 'HeatmapAnnotation' height(x, ...) <- value## S3 replacement method for class 'HeatmapAnnotation' height(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Height to the SingleAnnotation Object
## S3 replacement method for class 'SingleAnnotation' height(x, ...) <- value## S3 replacement method for class 'SingleAnnotation' height(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Height for annotation_axis Grob
## S3 method for class 'annotation_axis' heightDetails(x)## S3 method for class 'annotation_axis' heightDetails(x)
x |
The |
The physical height of the grob can be get by convertWidth(grobHeight(axis_grob), "mm").
# There is no example NULL# There is no example NULL
Grob height for packed_legends
## S3 method for class 'legend' heightDetails(x)## S3 method for class 'legend' heightDetails(x)
x |
A legend object. |
# There is no example NULL# There is no example NULL
Grob height for legend_body
## S3 method for class 'legend_body' heightDetails(x)## S3 method for class 'legend_body' heightDetails(x)
x |
A legend_body object. |
# There is no example NULL# There is no example NULL
Grob height for packed_legends
## S3 method for class 'packed_legends' heightDetails(x)## S3 method for class 'packed_legends' heightDetails(x)
x |
A packed_legends object. |
# There is no example NULL# There is no example NULL
Height for textbox grob
## S3 method for class 'textbox' heightDetails(x)## S3 method for class 'textbox' heightDetails(x)
x |
The |
A unit object.
# There is no example NULL# There is no example NULL
Global Options for Heatmaps
ht_global_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)ht_global_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)
... |
Options. |
RESET |
Reset all the option values. |
READ.ONLY |
|
LOCAL |
Wwitch to local mode. |
ADD |
Add new options. |
This function is deprecated. Please use ht_opt instead. However, changes by this function
will also be sychronized in ht_opt.
# There is no example NULL# There is no example NULL
Global Options for Heatmaps
ht_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)ht_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)
... |
Options, see 'Details' section. |
RESET |
Reset all the option values. |
READ.ONLY |
Please ignore this argument. |
LOCAL |
Please ignore this argument. |
ADD |
Please ignore this argument. |
You can set some parameters for all heatmaps/annotations simultaneously by this global function. Pleast note you should put it before your heatmap code and reset all option values after drawing the heatmaps to get rid of affecting next heatmap.
There are following parameters to control all heatmaps:
set row_names_gp in all Heatmap.
set column_names_gp in all Heatmap.
set row_title_gp in all Heatmap.
set column_title_gp in all Heatmap.
set border in all Heatmap.
Following parameters control the legends:
set title_gp in all heatmap legends and annotation legends.
set title_position in all heatmap legends and annotation legends.
set labels_gp in all heatmap legends and annotation legends.
set grid_width in all heatmap legends and annotation legends.
set grid_height in all heatmap legends and annotation legends.
set border in all heatmap legends and annotation legends.
Gap between legends. The value should be a vector of two units. One for gaps between vertical legends and one for the horizontal legends. If only one single unit is specified, the same gap set for the vertical and horizontal legends.
wether merge heatmap and annotation legends.
Following parameters control heatmap annotations:
border in all HeatmapAnnotation.
size for the simple annotation.
Following parameters control the space between heatmap components:
space bewteen dendrograms and heatmap body.
space between row/column names and heatmap body.
space between row/column titles and heatmap body. The value can have length of two which corresponds to the botton and top padding.
space between column annotations and heatmap body.
space between row annotations and heatmap body.
space between heatmap legends and heatmaps
space between annotation legends and heatmaps
Other parameters:
whether use hclust to speed up clustering?
when heatmap is split, whether to add a dashed line to mark parent dendrogram and children dendrograms?
default colors for continuous color mapping.
You can get or set option values by the traditional way (like options) or by $ operator:
# to get option values
ht_opt("heatmap_row_names_gp")
ht_opt$heatmap_row_names_gp
# to set option values
ht_opt("heatmap_row_names_gp" = gpar(fontsize = 8))
ht_opt$heatmap_row_names_gp = gpar(fontsize = 8)
Reset to the default values by ht_opt(RESET = TRUE).
Zuguang Gu <[email protected]>
ht_optht_opt
Calculate the width and height of the heatmaps
ht_size(ht)ht_size(ht)
ht |
A |
A list of two elements: width and height.
# There is no example NULL# There is no example NULL
Test Whether it is an Absolute Unit
is_abs_unit(u)is_abs_unit(u)
u |
A |
Besides the normal absolute units (e.g. "mm", "inches"), this function
simply assumes grob objects as absolute units.
For a complex unit which is combination of different units, it is absolute only if all units included are absolute units.
A logical value.
Zuguang Gu <[email protected]>
is_abs_unit(unit(1, "mm")) is_abs_unit(unit(1, "npc")) is_abs_unit(grobWidth(textGrob("foo"))) is_abs_unit(unit(1, "mm") + unit(1, "npc"))is_abs_unit(unit(1, "mm")) is_abs_unit(unit(1, "npc")) is_abs_unit(grobWidth(textGrob("foo"))) is_abs_unit(unit(1, "mm") + unit(1, "npc"))
Make a Single Legend
Legend(at, labels = at, col_fun, name = NULL, grob = NULL, break_dist = NULL, nrow = NULL, ncol = 1, by_row = FALSE, grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), tick_length = unit(0.8, "mm"), gap = unit(2, "mm"), column_gap = gap, row_gap = unit(0, "mm"), labels_gp = gpar(fontsize = 10), labels_rot = 0, border = NULL, background = "#EEEEEE", type = "grid", graphics = NULL, legend_gp = gpar(), pch = 16, size = unit(2, "mm"), legend_height = NULL, legend_width = NULL, direction = c("vertical", "horizontal"), title = "", title_gp = gpar(fontsize = 10, fontface = "bold"), title_position = c("topleft", "topcenter", "leftcenter", "lefttop", "leftcenter-rot", "lefttop-rot"), title_gap = unit(2, "mm"))Legend(at, labels = at, col_fun, name = NULL, grob = NULL, break_dist = NULL, nrow = NULL, ncol = 1, by_row = FALSE, grid_height = unit(4, "mm"), grid_width = unit(4, "mm"), tick_length = unit(0.8, "mm"), gap = unit(2, "mm"), column_gap = gap, row_gap = unit(0, "mm"), labels_gp = gpar(fontsize = 10), labels_rot = 0, border = NULL, background = "#EEEEEE", type = "grid", graphics = NULL, legend_gp = gpar(), pch = 16, size = unit(2, "mm"), legend_height = NULL, legend_width = NULL, direction = c("vertical", "horizontal"), title = "", title_gp = gpar(fontsize = 10, fontface = "bold"), title_position = c("topleft", "topcenter", "leftcenter", "lefttop", "leftcenter-rot", "lefttop-rot"), title_gap = unit(2, "mm"))
at |
Breaks of the legend. The values can be either numeric or character. If it is not specified, the values of |
labels |
Labels corresponding to |
col_fun |
A color mapping function which is used to make a continuous legend. Use |
name |
Name of the legend, internally used. |
grob |
The legend body can be specified by a pre-constructed |
break_dist |
A zooming factor to control relative distance of two neighbouring break values.The length of it should be |
nrow |
For legend which is represented as grids, |
ncol |
Similar as |
by_row |
Are the legend grids arranged by rows or by columns? |
grid_height |
The height of legend grid. It can also control the height of the continuous legend if it is horizontal. |
grid_width |
The width of legend grid. It can also control the width of the continuous legend if it is vertical. |
tick_length |
Length of the ticks on the continuous legends. Value should be a |
gap |
If legend grids are put into multiple rows or columns, this controls the gap between neighbouring rows or columns, measured as a |
column_gap |
The same as |
row_gap |
Space between legend rows. |
labels_gp |
Graphic parameters for labels. |
labels_rot |
Text rotation for labels. It should only be used for horizontal continuous legend. |
border |
Color of legend grid borders. It also works for the ticks in the continuous legend. |
background |
Background colors for the grids. It is used when points and lines are the legend graphics. |
type |
Type of legends. The value can be one of |
graphics |
Self-defined graphics for legends. The value should be a list of functions. Each function should accept four argumets: |
legend_gp |
Graphic parameters for the legend grids. You should control the filled color of the legend grids by |
pch |
Type of points if points are used as legend. Note you can use single-letter as pch, e.g. |
size |
Size of points. |
legend_height |
Height of the whole legend body. It is only used for vertical continous legend. |
legend_width |
Width of the whole legend body. It is only used for horizontal continous legend. |
direction |
Direction of the legend, vertical or horizontal? |
title |
Title of the legend. |
title_gp |
Graphic parameters of the title. |
title_position |
Position of title relative to the legend. |
title_gap |
Gap between title and the legend body. |
Most of the argument can also be set in heatmap_legend_param argument in Heatmap or annotation_legend_param
argument in HeatmapAnnotation to configure legend styles for heatmap and annotations.
A Legends-class object.
packLegend packs multiple legends into one Legends-class object.
See examples of configuring legends: https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html
lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6)) draw(lgd, test = "add labels and title") require(circlize) col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd = Legend(col_fun = col_fun, title = "foo") draw(lgd, test = "only col_fun") col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1)) draw(lgd, test = "unequal interval breaks")lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6)) draw(lgd, test = "add labels and title") require(circlize) col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd = Legend(col_fun = col_fun, title = "foo") draw(lgd, test = "only col_fun") col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd = Legend(col_fun = col_fun, title = "foo", at = c(0, 0.1, 0.15, 0.5, 0.9, 0.95, 1)) draw(lgd, test = "unequal interval breaks")
Constructor method for Legends class
Legends(...)Legends(...)
... |
arguments. |
There is no public constructor method for the Legends-class.
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
The Class for Legends
This is a very simple class for legends that it only has one slot which is the real grob of the legends.
Construct a single legend by Legend and a group of legends by packLegend.
lgd = Legend(at = 1:4) lgd lgd@groblgd = Legend(at = 1:4) lgd lgd@grob
Number of Annotations
## S3 method for class 'HeatmapAnnotation' length(x)## S3 method for class 'HeatmapAnnotation' length(x)
x |
A |
# There is no example NULL# There is no example NULL
Length of the HeatmapList object
## S3 method for class 'HeatmapList' length(x)## S3 method for class 'HeatmapList' length(x)
x |
A |
# There is no example NULL# There is no example NULL
List All Heatmap Components
list_components(pattern = NULL)list_components(pattern = NULL)
pattern |
A regular expression. |
A vector of viewport names.
# There is no example NULL# There is no example NULL
Convert a List of Sets to a Binary Matrix
list_to_matrix(lt, universal_set = NULL)list_to_matrix(lt, universal_set = NULL)
lt |
A list of vectors. |
universal_set |
The universal set. |
It converts the list which have m sets to a binary matrix with n rows and m columns where n is the size of universal set.
set.seed(123) lt = list(a = sample(letters, 5), b = sample(letters, 10), c = sample(letters, 15)) list_to_matrix(lt) list_to_matrix(lt, universal_set = letters)set.seed(123) lt = list(a = sample(letters, 5), b = sample(letters, 10), c = sample(letters, 15)) list_to_matrix(lt) list_to_matrix(lt, universal_set = letters)
Make Cluster on Columns
## S4 method for signature 'Heatmap' make_column_cluster(object)## S4 method for signature 'Heatmap' make_column_cluster(object)
object |
A |
The function will fill or adjust column_dend_list,
column_order_list, column_title and matrix_param slots.
If order is defined, no clustering will be applied.
This function is only for internal use.
A Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Make a Combination Matrix for UpSet Plot
make_comb_mat(..., mode = c("distinct", "intersect", "union"), top_n_sets = Inf, min_set_size = -Inf, universal_set = NULL, complement_size = NULL, value_fun = NULL, set_on_rows = TRUE)make_comb_mat(..., mode = c("distinct", "intersect", "union"), top_n_sets = Inf, min_set_size = -Inf, universal_set = NULL, complement_size = NULL, value_fun = NULL, set_on_rows = TRUE)
... |
The input sets. If it is represented as a single variable, it should be a matrix/data frame or a list. If it is multiple variables, it should be name-value pairs, see Input section for explanation. |
mode |
The mode for forming the combination set, see Mode section. |
top_n_sets |
Number of sets with largest size. |
min_set_size |
Ths minimal set size that is used for generating the combination matrix. |
universal_set |
The universal set. If it is set, the size of the complement set of all sets is also calculated. It if is specified, |
complement_size |
The size for the complement of all sets. If it is specified, the combination set name will be like "00...". |
value_fun |
For each combination set, how to calculate the size? If it is a scalar set, the length of the vector is the size of the set, while if it is a region-based set, (i.e. |
set_on_rows |
Used internally. |
A matrix also in a class of comb_mat.
Following functions can be applied to it: set_name, comb_name, set_size, comb_size, comb_degree,
extract_comb and t.comb_mat.
To represent multiple sets, the variable can be represented as:
1. A list of sets where each set is a vector, e.g.:
list(set1 = c("a", "b", "c"),
set2 = c("b", "c", "d", "e"),
...)
2. A binary matrix/data frame where rows are elements and columns are sets, e.g.:
a b c
h 1 1 1
t 1 0 1
j 1 0 0
u 1 0 1
w 1 0 0
...
If the variable is a data frame, the binary columns (only contain 0 and 1) and the logical columns are only kept.
The set can be genomic regions, then it can only be represented as a list of GRanges objects.
E.g. for three sets (A, B, C), the UpSet approach splits the combination of selecting elements in the set or not in the set and calculates the sizes of the combination sets. For three sets, all possible combinations are:
A B C
1 1 1
1 1 0
1 0 1
0 1 1
1 0 0
0 1 0
0 0 1
A value of 1 means to select that set and 0 means not to select that set. E.g., "1 1 0" means to select set A, B while not set C. Note there is no "0 0 0", because the background size is not of interest here. With the code of selecting and not selecting the sets, next we need to define how to calculate the size of that combination set. There are three modes:
1. distinct mode: 1 means in that set and 0 means not in that set, then "1 1 0" means a
set of elements also in set A and B, while not in C (i.e. setdiff(intersect(A, B), C)). Under
this mode, the seven combination sets are the seven partitions in the Venn diagram and they
are mutually exclusive.
2. intersect mode: 1 means in that set and 0 is not taken into account, then, "1 1 0" means
a set of elements in set A and B, and they can also in C or not in C (i.e. intersect(A, B)).
Under this mode, the seven combination sets can overlap.
3. union mode: 1 means in that set and 0 is not taken into account. When there are multiple
1, the relationship is OR. Then, "1 1 0" means a set of elements in set A or B, and they can also in C or not in C (i.e. union(A, B)).
Under this mode, the seven combination sets can overlap.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) mat = list_to_matrix(lt) mat m = make_comb_mat(mat) ## Not run: require(circlize) require(GenomicRanges) lt = lapply(1:4, function(i) generateRandomBed()) lt = lapply(lt, function(df) GRanges(seqnames = df[, 1], ranges = IRanges(df[, 2], df[, 3]))) names(lt) = letters[1:4] m = make_comb_mat(lt) ## End(Not run)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) mat = list_to_matrix(lt) mat m = make_comb_mat(mat) ## Not run: require(circlize) require(GenomicRanges) lt = lapply(1:4, function(i) generateRandomBed()) lt = lapply(lt, function(df) GRanges(seqnames = df[, 1], ranges = IRanges(df[, 2], df[, 3]))) names(lt) = letters[1:4] m = make_comb_mat(lt) ## End(Not run)
Method dispatch page for make_layout.
make_layout can be dispatched on following classes:
make_layout,Heatmap-method, Heatmap-class class method
make_layout,HeatmapList-method, HeatmapList-class class method
# no example NULL# no example NULL
Make the Layout of a Single Heatmap
## S4 method for signature 'Heatmap' make_layout(object)## S4 method for signature 'Heatmap' make_layout(object)
object |
A |
The layout of the single heatmap will be established by setting the size of each heatmap component. Also how to make graphics for heatmap components will be recorded by saving as functions.
Whether to apply row clustering or column clustering affects the layout, so clustering should be applied
first by prepare,Heatmap-method before making the layout.
This function is only for internal use.
A Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Make Layout for the Heatmap List
## S4 method for signature 'HeatmapList' make_layout(object, row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 14), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 14), heatmap_legend_side = c("right", "left", "bottom", "top"), merge_legends = FALSE, show_heatmap_legend = TRUE, heatmap_legend_list = list(), annotation_legend_side = c("right", "left", "bottom", "top"), show_annotation_legend = TRUE, annotation_legend_list = list(), align_heatmap_legend = NULL, align_annotation_legend = NULL, legend_grouping = c("adjusted", "original"), ht_gap = unit(2, "mm"), main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1], padding = GLOBAL_PADDING, auto_adjust = TRUE, row_dend_side = c("original", "left", "right"), row_sub_title_side = c("original", "left", "right"), column_dend_side = c("original", "top", "bottom"), column_sub_title_side = c("original", "top", "bottom"), row_gap = NULL, cluster_rows = NULL, cluster_row_slices = NULL, clustering_distance_rows = NULL, clustering_method_rows = NULL, row_dend_width = NULL, show_row_dend = NULL, row_dend_reorder = NULL, row_dend_gp = NULL, row_order = NULL, row_km = NULL, row_km_repeats = NULL, row_split = NULL, height = NULL, heatmap_height = NULL, column_gap = NULL, cluster_columns = NULL, cluster_column_slices = NULL, clustering_distance_columns = NULL, clustering_method_columns = NULL, column_dend_width = NULL, show_column_dend = NULL, column_dend_reorder = NULL, column_dend_gp = NULL, column_order = NULL, column_km = NULL, column_km_repeats = NULL, column_split = NULL, width = NULL, heatmap_width = NULL, use_raster = NULL, raster_device = NULL, raster_quality = NULL, raster_device_param = NULL, raster_resize = NULL)## S4 method for signature 'HeatmapList' make_layout(object, row_title = character(0), row_title_side = c("left", "right"), row_title_gp = gpar(fontsize = 14), column_title = character(0), column_title_side = c("top", "bottom"), column_title_gp = gpar(fontsize = 14), heatmap_legend_side = c("right", "left", "bottom", "top"), merge_legends = FALSE, show_heatmap_legend = TRUE, heatmap_legend_list = list(), annotation_legend_side = c("right", "left", "bottom", "top"), show_annotation_legend = TRUE, annotation_legend_list = list(), align_heatmap_legend = NULL, align_annotation_legend = NULL, legend_grouping = c("adjusted", "original"), ht_gap = unit(2, "mm"), main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1], padding = GLOBAL_PADDING, auto_adjust = TRUE, row_dend_side = c("original", "left", "right"), row_sub_title_side = c("original", "left", "right"), column_dend_side = c("original", "top", "bottom"), column_sub_title_side = c("original", "top", "bottom"), row_gap = NULL, cluster_rows = NULL, cluster_row_slices = NULL, clustering_distance_rows = NULL, clustering_method_rows = NULL, row_dend_width = NULL, show_row_dend = NULL, row_dend_reorder = NULL, row_dend_gp = NULL, row_order = NULL, row_km = NULL, row_km_repeats = NULL, row_split = NULL, height = NULL, heatmap_height = NULL, column_gap = NULL, cluster_columns = NULL, cluster_column_slices = NULL, clustering_distance_columns = NULL, clustering_method_columns = NULL, column_dend_width = NULL, show_column_dend = NULL, column_dend_reorder = NULL, column_dend_gp = NULL, column_order = NULL, column_km = NULL, column_km_repeats = NULL, column_split = NULL, width = NULL, heatmap_width = NULL, use_raster = NULL, raster_device = NULL, raster_quality = NULL, raster_device_param = NULL, raster_resize = NULL)
object |
A |
row_title |
Title on the row. |
row_title_side |
Will the title be put on the left or right of the heatmap list? |
row_title_gp |
Graphic parameters for the row title. |
column_title |
Title on the column. |
column_title_side |
Will the title be put on the top or bottom of the heatmap? |
column_title_gp |
Graphic parameters for the column title. |
heatmap_legend_side |
Side of the heatmap legends. |
merge_legends |
Whether to put heatmap legends and annotation legends together. By default they are put in different viewports. |
show_heatmap_legend |
Whether show heatmap legends. |
heatmap_legend_list |
A list of self-defined legends, should be wrapped into a list of |
annotation_legend_side |
Side of annotation legends. |
show_annotation_legend |
Whether show annotation legends. |
annotation_legend_list |
A list of self-defined legends, should be wrapped into a list of |
align_heatmap_legend |
How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is |
align_annotation_legend |
How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". |
legend_grouping |
How the legends are grouped. Values should be "adjusted" or "original". |
ht_gap |
Gap between heatmaps, should be a |
main_heatmap |
Name or index for the main heatmap. |
padding |
Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings. |
auto_adjust |
whether apply automatic adjustment? The auto-adjustment includes turning off dendrograms, titles and row/columns for non-main heatmaps. |
row_dend_side |
If auto-adjustment is on, to put the row dendrograms of the main heatmap to the most left side of the heatmap list or the most right side? |
row_sub_title_side |
There can be sub titles generated by the splitting of heatmaps. Similar setting as |
column_dend_side |
Similar setting as |
column_sub_title_side |
Similar setting as |
row_gap |
Overwrite the corresponding setting in the main heatmap. |
cluster_rows |
Overwrite the corresponding setting in the main heatmap. |
cluster_row_slices |
Overwrite the corresponding setting in the main heatmap. |
clustering_distance_rows |
Overwrite the corresponding setting in the main heatmap. |
clustering_method_rows |
Overwrite the corresponding setting in the main heatmap.same setting as in |
row_dend_width |
Overwrite the corresponding setting in the main heatmap. |
show_row_dend |
same Overwrite the corresponding setting in the main heatmap. |
row_dend_reorder |
Overwrite the corresponding setting in the main heatmap. |
row_dend_gp |
Overwrite the corresponding setting in the main heatmap. |
row_order |
Overwrite the corresponding setting in the main heatmap. |
row_km |
Overwrite the corresponding setting in the main heatmap. |
row_km_repeats |
Overwrite the corresponding setting in the main heatmap. |
row_split |
Overwrite the corresponding setting in the main heatmap. |
height |
Overwrite the corresponding setting in the main heatmap. |
heatmap_height |
Overwrite the corresponding setting in the main heatmap. |
column_gap |
Overwrite the corresponding setting in the main heatmap. |
cluster_columns |
Overwrite the corresponding setting in the main heatmap. |
cluster_column_slices |
Overwrite the corresponding setting in the main heatmap. |
clustering_distance_columns |
Overwrite the corresponding setting in the main heatmap. |
clustering_method_columns |
Overwrite the corresponding setting in the main heatmap. |
column_dend_width |
column Overwrite the corresponding setting in the main heatmap. |
show_column_dend |
Overwrite the corresponding setting in the main heatmap. |
column_dend_reorder |
Overwrite the corresponding setting in the main heatmap. |
column_dend_gp |
Overwrite the corresponding setting in the main heatmap. |
column_order |
Overwrite the corresponding setting in the main heatmap. |
column_km |
Overwrite the corresponding setting in the main heatmap. |
column_km_repeats |
Overwrite the corresponding setting in the main heatmap. |
column_split |
Overwrite the corresponding setting in the main heatmap. |
width |
Overwrite the corresponding setting in the main heatmap. |
heatmap_width |
Overwrite the corresponding setting in the main heatmap. |
use_raster |
Overwrite the corresponding setting in every heatmap. |
raster_device |
Overwrite the corresponding setting in every heatmap. |
raster_quality |
Overwrite the corresponding setting in every heatmap. |
raster_device_param |
Overwrite the corresponding setting in every heatmap. |
raster_resize |
Overwrite the corresponding setting in every heatmap. |
It sets the size of each component of the heatmap list and adjusts graphic parameters for each heatmap if necessary.
This function is only for internal use.
A HeatmapList-class object in which settings for all heatmap are adjusted.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Make Cluster on Rows
## S4 method for signature 'Heatmap' make_row_cluster(object)## S4 method for signature 'Heatmap' make_row_cluster(object)
object |
A |
The function will fill or adjust row_dend_list, row_order_list, row_title and matrix_param slots.
If order is defined, no clustering will be applied.
This function is only for internal use.
A Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Map Values to Colors
## S4 method for signature 'ColorMapping' map_to_colors(object, x)## S4 method for signature 'ColorMapping' map_to_colors(object, x)
object |
A |
x |
Input values. |
It maps a vector of values to a vector of colors.
This function provides a uniform way for discrete and continuous color mapping.
A vector of colors.
Zuguang Gu <[email protected]>
cm = ColorMapping(colors = c("A" = "red", "B" = "black")) map_to_colors(cm, sample(c("A", "B"), 10, replace = TRUE)) require(circlize) col_fun = colorRamp2(c(0, 1), c("white", "red")) cm = ColorMapping(col_fun = col_fun) map_to_colors(cm, runif(10))cm = ColorMapping(colors = c("A" = "red", "B" = "black")) map_to_colors(cm, sample(c("A", "B"), 10, replace = TRUE)) require(circlize) col_fun = colorRamp2(c(0, 1), c("white", "red")) cm = ColorMapping(col_fun = col_fun) map_to_colors(cm, runif(10))
Maximum Height of Text
max_text_height(text, gp = gpar(), rot = 0)max_text_height(text, gp = gpar(), rot = 0)
text |
A vector of text. |
gp |
Graphic parameters for text. |
rot |
Rotation of the text, scalar. |
It simply calculates maximum height of a list of textGrob objects.
Note it ignores the text rotation.
A unit object.
Zuguang Gu <[email protected]>
max_text_width calculates the maximum width of a text vector.
x = c("a", "b\nb", "c\nc\nc") max_text_height(x, gp = gpar(fontsize = 10))x = c("a", "b\nb", "c\nc\nc") max_text_height(x, gp = gpar(fontsize = 10))
Maximum Width of Text
max_text_width(text, gp = gpar(), rot = 0)max_text_width(text, gp = gpar(), rot = 0)
text |
A vector of text. |
gp |
Graphic parameters for text. |
rot |
Rotation of the text, scalar. |
It simply calculates maximum width of a list of textGrob objects.
Note it ignores the text rotation.
A unit object which is in "mm".
Zuguang Gu <[email protected]>
max_text_height calculates the maximum height of a text vector.
x = c("a", "bb", "ccc") max_text_width(x, gp = gpar(fontsize = 10))x = c("a", "bb", "ccc") max_text_width(x, gp = gpar(fontsize = 10))
Merge Dendrograms
merge_dendrogram(x, y, only_parent = FALSE, ...)merge_dendrogram(x, y, only_parent = FALSE, ...)
x |
The parent dendrogram. |
y |
The children dendrograms. They are connected to the leaves of the parent dendrogram. So the length of |
only_parent |
Whether only returns the parent dendrogram where the height and node positions have been adjusted by children dendrograms. |
... |
Other arguments. |
Do not retrieve the order of the merged dendrogram. It is not reliable.
m1 = matrix(rnorm(100), nr = 10) m2 = matrix(rnorm(80), nr = 8) m3 = matrix(rnorm(50), nr = 5) dend1 = as.dendrogram(hclust(dist(m1))) dend2 = as.dendrogram(hclust(dist(m2))) dend3 = as.dendrogram(hclust(dist(m3))) dend_p = as.dendrogram(hclust(dist(rbind(colMeans(m1), colMeans(m2), colMeans(m3))))) dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3)) grid.dendrogram(dend_m, test = TRUE) dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3), only_parent = TRUE) grid.dendrogram(dend_m, test = TRUE) require(dendextend) dend1 = color_branches(dend1, k = 1, col = "red") dend2 = color_branches(dend2, k = 1, col = "blue") dend3 = color_branches(dend3, k = 1, col = "green") dend_p = color_branches(dend_p, k = 1, col = "orange") dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3)) grid.dendrogram(dend_m, test = TRUE)m1 = matrix(rnorm(100), nr = 10) m2 = matrix(rnorm(80), nr = 8) m3 = matrix(rnorm(50), nr = 5) dend1 = as.dendrogram(hclust(dist(m1))) dend2 = as.dendrogram(hclust(dist(m2))) dend3 = as.dendrogram(hclust(dist(m3))) dend_p = as.dendrogram(hclust(dist(rbind(colMeans(m1), colMeans(m2), colMeans(m3))))) dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3)) grid.dendrogram(dend_m, test = TRUE) dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3), only_parent = TRUE) grid.dendrogram(dend_m, test = TRUE) require(dendextend) dend1 = color_branches(dend1, k = 1, col = "red") dend2 = color_branches(dend2, k = 1, col = "blue") dend3 = color_branches(dend3, k = 1, col = "green") dend_p = color_branches(dend_p, k = 1, col = "orange") dend_m = merge_dendrogram(dend_p, list(dend1, dend2, dend3)) grid.dendrogram(dend_m, test = TRUE)
Annotation Names
## S3 method for class 'HeatmapAnnotation' names(x)## S3 method for class 'HeatmapAnnotation' names(x)
x |
A |
ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1)) names(ha)ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1)) names(ha)
Names of the heatmaps/annotations
## S3 method for class 'HeatmapList' names(x)## S3 method for class 'HeatmapList' names(x)
x |
A |
# There is no example NULL# There is no example NULL
Assign Annotation Names
## S3 replacement method for class 'HeatmapAnnotation' names(x) <- value## S3 replacement method for class 'HeatmapAnnotation' names(x) <- value
x |
A |
value |
A vector of new names. |
ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1)) names(ha) = c("A", "B") names(ha)ha = HeatmapAnnotation(foo = 1:10, bar = anno_points(10:1)) names(ha) = c("A", "B") names(ha)
Number of Columns in the Heatmap
## S3 method for class 'Heatmap' ncol(x)## S3 method for class 'Heatmap' ncol(x)
x |
A |
# There is no example NULL# There is no example NULL
Number of Observations
## S3 method for class 'AnnotationFunction' nobs(object, ...)## S3 method for class 'AnnotationFunction' nobs(object, ...)
object |
The |
... |
Other arguments. |
returns NA.
anno = anno_points(1:10) nobs(anno)anno = anno_points(1:10) nobs(anno)
Number of Observations
## S3 method for class 'HeatmapAnnotation' nobs(object, ...)## S3 method for class 'HeatmapAnnotation' nobs(object, ...)
object |
The |
... |
other arguments. |
If there is no nobs information for any of its SingleAnnotation-class object,
it returns NA.
# There is no example NULL# There is no example NULL
Number of Observations
## S3 method for class 'SingleAnnotation' nobs(object, ...)## S3 method for class 'SingleAnnotation' nobs(object, ...)
object |
The |
... |
Other arguments. |
It returns the n slot of the annotaton function. If it does not exist, it returns NA.
# There is no example NULL# There is no example NULL
Normalize a list of combination matrice
normalize_comb_mat(..., full_comb_sets = FALSE, complement_set = FALSE)normalize_comb_mat(..., full_comb_sets = FALSE, complement_set = FALSE)
... |
Combination matrices. |
full_comb_sets |
Whether the combination matrices contain the full sets of combination sets? |
complement_set |
Whether the combination matrices also contain the complement set? |
It normalizes a list of combination matrice to make them have same number and order of sets and combination sets.
The sets (by set_name) from all combination matrice should be the same.
# There is no example NULL# There is no example NULL
Overlap genomic signals to the genomic bins
normalize_genomic_signals_to_bins(gr, value, value_column = NULL, method = "weighted", empty_value = NA, window = GHEATMAP_ENV$chr_window)normalize_genomic_signals_to_bins(gr, value, value_column = NULL, method = "weighted", empty_value = NA, window = GHEATMAP_ENV$chr_window)
gr |
A |
value |
The corresponding signals corresponding to |
value_column |
If |
method |
One of "weighted", "w0" and "absolute". For the three different methods, please refer to https://bioconductor.org/packages/release/bioc/vignettes/EnrichedHeatmap/inst/doc/EnrichedHeatmap.html#toc_7 . |
empty_value |
The value for the bins where no signal is overlapped. |
window |
The genomic bins generated from |
The genomic bins should be generated by bin_genome in advance. The genomic bins are saved internally, so that multiple
uses of bin_genome ensure they all return the matrices with the same rows.
It supports following values.
When neither value nor value_column is set, it simply overlap gr to the genomic bins and returns a one-column logical matrix which represents whether the current genomic bin overlaps to any signal.
When the signals are numeric, value can be a numeric vector or a matrix, or value_column can contain multiple columns. The function returns a numeric matrix where the values are properly averaged depending on what method was used.
When the signals are character, value can only be a vector or value_column can only contain one single column. The function returns a one-column character matrix.
A matrix with the same row as the genomic bins.
## Not run: require(circlize) require(GenomicRanges) chr_window = bin_genome("hg19") #### the first is a numeric matrix ####### bed1 = generateRandomBed(nr = 1000, nc = 10) gr1 = GRanges(seqnames = bed1[, 1], ranges = IRanges(bed1[, 2], bed1[, 3])) num_mat = normalize_genomic_signals_to_bins(gr1, bed1[, -(1:3)]) #### the second is a character matrix ###### bed_list = lapply(1:10, function(i) { generateRandomBed(nr = 1000, nc = 1, fun = function(n) sample(c("gain", "loss"), n, replace = TRUE)) }) char_mat = NULL for(i in 1:10) { bed = bed_list[[i]] bed = bed[sample(nrow(bed), 20), , drop = FALSE] gr_cnv = GRanges(seqnames = bed[, 1], ranges = IRanges(bed[, 2], bed[, 3])) char_mat = cbind(char_mat, normalize_genomic_signals_to_bins(gr_cnv, bed[, 4])) } #### two numeric columns ########## bed2 = generateRandomBed(nr = 100, nc = 2) gr2 = GRanges(seqnames = bed2[, 1], ranges = IRanges(bed2[, 2], bed2[, 3])) v = normalize_genomic_signals_to_bins(gr2, bed2[, 4:5]) ##### a list of genes need to be highlighted bed3 = generateRandomBed(nr = 40, nc = 0) gr3 = GRanges(seqnames = bed3[, 1], ranges = IRanges(bed3[, 2], bed3[, 2])) gr3$gene = paste0("gene_", 1:length(gr3)) mtch = as.matrix(findOverlaps(chr_window, gr3)) at = mtch[, 1] labels = mcols(gr3)[mtch[, 2], 1] ##### order of the chromosomes ######## chr = as.vector(seqnames(chr_window)) chr_level = paste0("chr", c(1:22, "X", "Y")) chr = factor(chr, levels = chr_level) #### make the heatmap ####### subgroup = rep(c("A", "B"), each = 5) ht_opt$TITLE_PADDING = unit(c(4, 4), "points") ht_list = Heatmap(num_mat, name = "mat", col = colorRamp2(c(-1, 0, 1), c("green", "white", "red")), row_split = chr, cluster_rows = FALSE, show_column_dend = FALSE, column_split = subgroup, cluster_column_slices = FALSE, column_title = "numeric matrix", top_annotation = HeatmapAnnotation(subgroup = subgroup, annotation_name_side = "left"), row_title_rot = 0, row_title_gp = gpar(fontsize = 10), border = TRUE, row_gap = unit(0, "points")) + Heatmap(char_mat, name = "CNV", col = c("gain" = "red", "loss" = "blue"), border = TRUE, column_title = "character matrix") + rowAnnotation(label = anno_mark(at = at, labels = labels)) + rowAnnotation(pt = anno_points(v, gp = gpar(col = 4:5), pch = c(1, 16)), width = unit(2, "cm")) + rowAnnotation(bar = anno_barplot(v[, 1], gp = gpar(col = ifelse(v[ ,1] > 0, 2, 3))), width = unit(2, "cm")) draw(ht_list, merge_legend = TRUE) ##### or horizontally ### ht_list = Heatmap(t(num_mat), name = "mat", col = colorRamp2(c(-1, 0, 1), c("green", "white", "red")), column_split = chr, cluster_columns = FALSE, show_row_dend = FALSE, row_split = subgroup, cluster_row_slices = FALSE, row_title = "numeric matrix", left_annotation = rowAnnotation(subgroup = subgroup, show_annotation_name = FALSE, annotation_legend_param = list( subgroup = list(direction = "horizontal", title_position = "lefttop", nrow = 1))), column_title_gp = gpar(fontsize = 10), border = TRUE, column_gap = unit(0, "points"), column_title = ifelse(seq_along(chr_level) %% 2 == 0, paste0("\n", chr_level), paste0(chr_level, "\n")), heatmap_legend_param = list(direction = "horizontal", title_position = "lefttop")) %v% Heatmap(t(char_mat), name = "CNV", col = c("gain" = "red", "loss" = "blue"), border = TRUE, row_title = "character matrix", heatmap_legend_param = list(direction = "horizontal", title_position = "lefttop", nrow = 1)) %v% HeatmapAnnotation(label = anno_mark(at = at, labels = labels, side = "bottom")) %v% HeatmapAnnotation(pt = anno_points(v, gp = gpar(col = 4:5), pch = c(1, 16)), annotation_name_side = "left", height = unit(2, "cm")) %v% HeatmapAnnotation(bar = anno_barplot(v[, 1], gp = gpar(col = ifelse(v[ ,1] > 0, 2, 3))), annotation_name_side = "left", height = unit(2, "cm")) draw(ht_list, heatmap_legend_side = "bottom", merge_legend = TRUE) ## End(Not run)## Not run: require(circlize) require(GenomicRanges) chr_window = bin_genome("hg19") #### the first is a numeric matrix ####### bed1 = generateRandomBed(nr = 1000, nc = 10) gr1 = GRanges(seqnames = bed1[, 1], ranges = IRanges(bed1[, 2], bed1[, 3])) num_mat = normalize_genomic_signals_to_bins(gr1, bed1[, -(1:3)]) #### the second is a character matrix ###### bed_list = lapply(1:10, function(i) { generateRandomBed(nr = 1000, nc = 1, fun = function(n) sample(c("gain", "loss"), n, replace = TRUE)) }) char_mat = NULL for(i in 1:10) { bed = bed_list[[i]] bed = bed[sample(nrow(bed), 20), , drop = FALSE] gr_cnv = GRanges(seqnames = bed[, 1], ranges = IRanges(bed[, 2], bed[, 3])) char_mat = cbind(char_mat, normalize_genomic_signals_to_bins(gr_cnv, bed[, 4])) } #### two numeric columns ########## bed2 = generateRandomBed(nr = 100, nc = 2) gr2 = GRanges(seqnames = bed2[, 1], ranges = IRanges(bed2[, 2], bed2[, 3])) v = normalize_genomic_signals_to_bins(gr2, bed2[, 4:5]) ##### a list of genes need to be highlighted bed3 = generateRandomBed(nr = 40, nc = 0) gr3 = GRanges(seqnames = bed3[, 1], ranges = IRanges(bed3[, 2], bed3[, 2])) gr3$gene = paste0("gene_", 1:length(gr3)) mtch = as.matrix(findOverlaps(chr_window, gr3)) at = mtch[, 1] labels = mcols(gr3)[mtch[, 2], 1] ##### order of the chromosomes ######## chr = as.vector(seqnames(chr_window)) chr_level = paste0("chr", c(1:22, "X", "Y")) chr = factor(chr, levels = chr_level) #### make the heatmap ####### subgroup = rep(c("A", "B"), each = 5) ht_opt$TITLE_PADDING = unit(c(4, 4), "points") ht_list = Heatmap(num_mat, name = "mat", col = colorRamp2(c(-1, 0, 1), c("green", "white", "red")), row_split = chr, cluster_rows = FALSE, show_column_dend = FALSE, column_split = subgroup, cluster_column_slices = FALSE, column_title = "numeric matrix", top_annotation = HeatmapAnnotation(subgroup = subgroup, annotation_name_side = "left"), row_title_rot = 0, row_title_gp = gpar(fontsize = 10), border = TRUE, row_gap = unit(0, "points")) + Heatmap(char_mat, name = "CNV", col = c("gain" = "red", "loss" = "blue"), border = TRUE, column_title = "character matrix") + rowAnnotation(label = anno_mark(at = at, labels = labels)) + rowAnnotation(pt = anno_points(v, gp = gpar(col = 4:5), pch = c(1, 16)), width = unit(2, "cm")) + rowAnnotation(bar = anno_barplot(v[, 1], gp = gpar(col = ifelse(v[ ,1] > 0, 2, 3))), width = unit(2, "cm")) draw(ht_list, merge_legend = TRUE) ##### or horizontally ### ht_list = Heatmap(t(num_mat), name = "mat", col = colorRamp2(c(-1, 0, 1), c("green", "white", "red")), column_split = chr, cluster_columns = FALSE, show_row_dend = FALSE, row_split = subgroup, cluster_row_slices = FALSE, row_title = "numeric matrix", left_annotation = rowAnnotation(subgroup = subgroup, show_annotation_name = FALSE, annotation_legend_param = list( subgroup = list(direction = "horizontal", title_position = "lefttop", nrow = 1))), column_title_gp = gpar(fontsize = 10), border = TRUE, column_gap = unit(0, "points"), column_title = ifelse(seq_along(chr_level) %% 2 == 0, paste0("\n", chr_level), paste0(chr_level, "\n")), heatmap_legend_param = list(direction = "horizontal", title_position = "lefttop")) %v% Heatmap(t(char_mat), name = "CNV", col = c("gain" = "red", "loss" = "blue"), border = TRUE, row_title = "character matrix", heatmap_legend_param = list(direction = "horizontal", title_position = "lefttop", nrow = 1)) %v% HeatmapAnnotation(label = anno_mark(at = at, labels = labels, side = "bottom")) %v% HeatmapAnnotation(pt = anno_points(v, gp = gpar(col = 4:5), pch = c(1, 16)), annotation_name_side = "left", height = unit(2, "cm")) %v% HeatmapAnnotation(bar = anno_barplot(v[, 1], gp = gpar(col = ifelse(v[ ,1] > 0, 2, 3))), annotation_name_side = "left", height = unit(2, "cm")) draw(ht_list, heatmap_legend_side = "bottom", merge_legend = TRUE) ## End(Not run)
Number of Rows in the Heatmap
## S3 method for class 'Heatmap' nrow(x)## S3 method for class 'Heatmap' nrow(x)
x |
A |
# There is no example NULL# There is no example NULL
Make oncoPrint
oncoPrint(mat, name, get_type = default_get_type, alter_fun, alter_fun_is_vectorized = NULL, col = NULL, top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot()), right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot()), left_annotation = NULL, bottom_annotation = NULL, show_pct = TRUE, pct_gp = gpar(fontsize = 10), pct_digits = 0, pct_side = "left", pct_include = NULL, row_labels = NULL, show_row_names = TRUE, row_names_side = "right", row_names_gp = pct_gp, row_split = NULL, column_labels = NULL, column_names_gp = gpar(fontsize = 10), column_split = NULL, row_order = NULL, column_order = NULL, cluster_rows = FALSE, cluster_columns = FALSE, remove_empty_columns = FALSE, remove_empty_rows = FALSE, show_column_names = FALSE, heatmap_legend_param = NULL, ...)oncoPrint(mat, name, get_type = default_get_type, alter_fun, alter_fun_is_vectorized = NULL, col = NULL, top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot()), right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot()), left_annotation = NULL, bottom_annotation = NULL, show_pct = TRUE, pct_gp = gpar(fontsize = 10), pct_digits = 0, pct_side = "left", pct_include = NULL, row_labels = NULL, show_row_names = TRUE, row_names_side = "right", row_names_gp = pct_gp, row_split = NULL, column_labels = NULL, column_names_gp = gpar(fontsize = 10), column_split = NULL, row_order = NULL, column_order = NULL, cluster_rows = FALSE, cluster_columns = FALSE, remove_empty_columns = FALSE, remove_empty_rows = FALSE, show_column_names = FALSE, heatmap_legend_param = NULL, ...)
mat |
The value should be a character matrix which encodes mulitple alterations or a list of matrices for which every matrix contains binary value representing whether the alteration is present or absent. When the value is a list, the names of the list represent alteration types. You can use |
name |
Name of the oncoPrint. Not necessary to specify. |
get_type |
If different alterations are encoded in the matrix as complex strings, this self-defined function determines how to extract them. It only works when |
alter_fun |
A single function or a list of functions which defines how to add graphics for different alterations. You can use |
alter_fun_is_vectorized |
Whether |
col |
A vector of color for which names correspond to alteration types. |
top_annotation |
Annotation put on top of the oncoPrint. By default it is barplot which shows the number of genes with a certain alteration in each sample. |
right_annotation |
Annotation put on the right of the oncoPrint. By default it is barplot which shows the number of samples with a certain alteration in each gene. |
left_annotation |
Annotation put on the left of the oncoPrint. |
bottom_annotation |
Annotation put at the bottom of the oncoPrint. |
show_pct |
whether show percent values on the left of the oncoprint? |
pct_gp |
Graphic paramters for percent values |
pct_digits |
Digits for the percent values. |
pct_side |
Side of the percent values to the oncoPrint. This argument is currently disabled. |
pct_include |
Alteration types that are included for the calculation of percent values. |
row_labels |
Labels as the row names of the oncoPrint. |
show_row_names |
Whether show row names? |
row_names_side |
Side of the row names to the oncoPrint. This argument is currently disabled. |
row_names_gp |
Graphic parameters for the row names. |
row_split |
Pass to |
column_labels |
Pass to |
column_names_gp |
Pass to |
column_split |
Pass to |
row_order |
Order of rows. By default rows are sorted by the number of occurence of the alterations. |
cluster_rows |
If it is set, it must be a dendrogram/hclust object. |
cluster_columns |
If it is set, it must be a dendrogram/hclust object. |
column_order |
Order of columns. By default the columns are sorted to show the mutual exclusivity of alterations. |
remove_empty_columns |
If there is no alteration in some samples, whether remove them on the oncoPrint? |
remove_empty_rows |
If there is no alteration in some samples, whether remove them on the oncoPrint? |
show_column_names |
Whether show column names? |
heatmap_legend_param |
pass to |
... |
Pass to |
The 'memo sort' method is from https://gist.github.com/armish/564a65ab874a770e2c26 . Thanks to B. Arman Aksoy for contributing the code.
https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html gives details for configuring a oncoPrint.
A Heatmap-class object which means you can add other heatmaps or annotations to it.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Order of the Combination Sets
order.comb_mat(m, decreasing = TRUE, on = "comb_set")order.comb_mat(m, decreasing = TRUE, on = "comb_set")
m |
A combination matrix returned by |
on |
On sets or on combination sets? |
decreasing |
Whether the ordering is applied decreasingly. |
It first sorts by the degree of the combination sets then by the combination matrix.
# There is no example NULL# There is no example NULL
Pack Legends
packLegend(..., gap = unit(4, "mm"), row_gap = unit(4, "mm"), column_gap = unit(4, "mm"), direction = c("vertical", "horizontal"), max_width = NULL, max_height = NULL, list = NULL)packLegend(..., gap = unit(4, "mm"), row_gap = unit(4, "mm"), column_gap = unit(4, "mm"), direction = c("vertical", "horizontal"), max_width = NULL, max_height = NULL, list = NULL)
... |
A list of objects returned by |
gap |
Gap between two neighbouring legends. The value is a |
row_gap |
Horizontal gaps between legends. |
column_gap |
Vertical gaps between legends. |
direction |
The direction to arrange legends. |
max_width |
The maximal width of the total packed legends. It only works for horizontal arrangement. If the total width of the legends exceeds it, the legends will be arranged into multiple rows. |
max_height |
Similar as |
list |
The list of legends can be specified as a list. |
A Legends-class object.
https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#a-list-of-legends
require(circlize) col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd1 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1") lgd2 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1)) pd = packLegend(lgd1, lgd2) draw(pd, test = "two legends") pd = packLegend(lgd1, lgd2, direction = "horizontal") draw(pd, test = "two legends packed horizontally")require(circlize) col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red")) lgd1 = Legend(at = 1:6, legend_gp = gpar(fill = 1:6), title = "legend1") lgd2 = Legend(col_fun = col_fun, title = "legend2", at = c(0, 0.25, 0.5, 0.75, 1)) pd = packLegend(lgd1, lgd2) draw(pd, test = "two legends") pd = packLegend(lgd1, lgd2, direction = "horizontal") draw(pd, test = "two legends packed horizontally")
Translate pheatmap::pheatmap to ComplexHeatmap::Heatmap
pheatmap(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = ifelse(nrow(mat) < 100 & ncol(mat) < 100, "grey60", NA), cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete", clustering_callback = NA, cutree_rows = NA, cutree_cols = NA, treeheight_row = ifelse(class(cluster_rows) == "hclust" || cluster_rows, 50, 0), treeheight_col = ifelse(class(cluster_cols) == "hclust" || cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation_row = NA, annotation_col = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, annotation_names_row = TRUE, annotation_names_col = TRUE, drop_levels = TRUE, show_rownames = TRUE, show_colnames = TRUE, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, angle_col = c("270", "0", "45", "90", "315"), display_numbers = FALSE, number_format = "%.2f", number_color = "grey30", fontsize_number = 0.8 * fontsize, gaps_row = NULL, gaps_col = NULL, labels_row = NULL, labels_col = NULL, filename = NA, width = NA, height = NA, silent = FALSE, na_col = "#DDDDDD", name = NULL, # other graphic parameters for fonts fontfamily = "", fontfamily_row = fontfamily, fontfamily_col = fontfamily, fontface = 1, fontface_row = fontface, fontface_col = fontface, # argument specific for Heatmap() heatmap_legend_param = list(), ..., run_draw = FALSE)pheatmap(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = ifelse(nrow(mat) < 100 & ncol(mat) < 100, "grey60", NA), cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete", clustering_callback = NA, cutree_rows = NA, cutree_cols = NA, treeheight_row = ifelse(class(cluster_rows) == "hclust" || cluster_rows, 50, 0), treeheight_col = ifelse(class(cluster_cols) == "hclust" || cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation_row = NA, annotation_col = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, annotation_names_row = TRUE, annotation_names_col = TRUE, drop_levels = TRUE, show_rownames = TRUE, show_colnames = TRUE, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, angle_col = c("270", "0", "45", "90", "315"), display_numbers = FALSE, number_format = "%.2f", number_color = "grey30", fontsize_number = 0.8 * fontsize, gaps_row = NULL, gaps_col = NULL, labels_row = NULL, labels_col = NULL, filename = NA, width = NA, height = NA, silent = FALSE, na_col = "#DDDDDD", name = NULL, # other graphic parameters for fonts fontfamily = "", fontfamily_row = fontfamily, fontfamily_col = fontfamily, fontface = 1, fontface_row = fontface, fontface_col = fontface, # argument specific for Heatmap() heatmap_legend_param = list(), ..., run_draw = FALSE)
mat |
The input matrix. |
color |
The same as in |
kmeans_k |
The same as in |
breaks |
The same as in |
border_color |
The same as in |
cellwidth |
The same as in |
cellheight |
The same as in |
scale |
The same as in |
cluster_rows |
The same as in |
cluster_cols |
The same as in |
clustering_distance_rows |
The same as in |
clustering_distance_cols |
The same as in |
clustering_method |
The same as in |
clustering_callback |
The same as in |
cutree_rows |
The same as in |
cutree_cols |
The same as in |
treeheight_row |
The same as in |
treeheight_col |
The same as in |
legend |
The same as in |
legend_breaks |
The same as in |
legend_labels |
The same as in |
annotation_row |
The same as in |
annotation_col |
The same as in |
annotation |
The same as in |
annotation_colors |
The same as in |
annotation_legend |
The same as in |
annotation_names_row |
The same as in |
annotation_names_col |
The same as in |
drop_levels |
Enforced to be |
show_rownames |
The same as in |
show_colnames |
The same as in |
main |
The same as in |
fontsize |
The same as in |
fontsize_row |
The same as in |
fontsize_col |
The same as in |
angle_col |
The same as in |
display_numbers |
The same as in |
number_format |
The same as in |
number_color |
The same as in |
fontsize_number |
The same as in |
gaps_row |
The same as in |
gaps_col |
The same as in |
labels_row |
The same as in |
labels_col |
The same as in |
filename |
Not supported. |
width |
Not supported. |
height |
Not supported. |
silent |
Not supported. |
na_col |
The same as in |
name |
Name of the heatmap. This argument is passed to |
fontfamily |
Font family for row and column names. |
fontfamily_row |
Font family for row names. |
fontfamily_col |
Font family for column names. |
fontface |
Font face for row and column names. |
fontface_row |
Font face for row names. |
fontface_col |
Font face for column names. |
heatmap_legend_param |
Pass to |
... |
Other arguments passed to |
run_draw |
Whether to run |
This function aims to execute pheatmap::pheatmap code purely with ComplexHeatmap.
A Heatmap-class object.
See https://jokergoo.github.io/2020/05/06/translate-from-pheatmap-to-complexheatmap/
compare_pheatmap that compares heatmaps between pheatmap::pheatmap() and ComplexHeatmap::pheatmap().
# There is no example NULL# There is no example NULL
Get Values in a Matrix by Pair-wise Indices
pindex(m, i, j)pindex(m, i, j)
m |
A matrix or a 3-dimension array. |
i |
Row indices or the indices in the first dimension. |
j |
Column indicies or the indices in the second dimension. |
If m is a matrix, the value returned is a vector c(m[i1, j1], m[i2, j2], ...)'.
If m is an array, the value returned is a matrix rbind(m[i1, j1, ], m[i2, j2, ], ...)'.
m = matrix(rnorm(100), 10) m2 = m[m > 0] ind = do.call("rbind", lapply(1:10, function(ci) { i = which(m[, ci] > 0) cbind(i = i, j = rep(ci, length(i))) })) pindex(m, ind[, 1], ind[, 2]) identical(pindex(m, ind[, 1], ind[, 2]), m[m > 0]) # 3d array arr = array(1:27, dim = c(3, 3, 3)) pindex(arr, 1:2, 2:3) identical(pindex(arr, 1:2, 2:3), rbind(arr[1, 2, ], arr[2, 3, ]))m = matrix(rnorm(100), 10) m2 = m[m > 0] ind = do.call("rbind", lapply(1:10, function(ci) { i = which(m[, ci] > 0) cbind(i = i, j = rep(ci, length(i))) })) pindex(m, ind[, 1], ind[, 2]) identical(pindex(m, ind[, 1], ind[, 2]), m[m > 0]) # 3d array arr = array(1:27, dim = c(3, 3, 3)) pindex(arr, 1:2, 2:3) identical(pindex(arr, 1:2, 2:3), rbind(arr[1, 2, ], arr[2, 3, ]))
Draw heatmap
## S3 method for class 'Heatmap' plot(x, ...)## S3 method for class 'Heatmap' plot(x, ...)
x |
A |
... |
All pass to |
# There is no example NULL# There is no example NULL
Draw heatmap annotations
## S3 method for class 'HeatmapAnnotation' plot(x, ...)## S3 method for class 'HeatmapAnnotation' plot(x, ...)
x |
A |
... |
All pass to |
# There is no example NULL# There is no example NULL
Draw heatmap
## S3 method for class 'HeatmapList' plot(x, ...)## S3 method for class 'HeatmapList' plot(x, ...)
x |
A |
... |
All pass to |
# There is no example NULL# There is no example NULL
Prepare the Heatmap
## S4 method for signature 'Heatmap' prepare(object, process_rows = TRUE, process_columns = TRUE)## S4 method for signature 'Heatmap' prepare(object, process_rows = TRUE, process_columns = TRUE)
object |
A |
process_rows |
Whether to process rows of the heatmap. |
process_columns |
Whether to process columns of the heatmap. |
The preparation of the heatmap includes following steps:
making clustering on rows (by calling make_row_cluster,Heatmap-method)
making clustering on columns (by calling make_column_cluster,Heatmap-method)
making the layout of the heatmap (by calling make_layout,Heatmap-method)
This function is only for internal use.
The Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Print the comb_mat Object
## S3 method for class 'comb_mat' print(x, ...)## S3 method for class 'comb_mat' print(x, ...)
x |
A combination matrix returned by |
... |
Other arguments |
# There is no example NULL# There is no example NULL
Resize the Width or Height of Heatmap Annotations
## S4 method for signature 'HeatmapAnnotation' re_size(object, annotation_height = NULL, annotation_width = NULL, height = NULL, width = NULL, simple_anno_size = object@param$simple_anno_size, simple_anno_size_adjust = object@param$simple_anno_size_adjust)## S4 method for signature 'HeatmapAnnotation' re_size(object, annotation_height = NULL, annotation_width = NULL, height = NULL, width = NULL, simple_anno_size = object@param$simple_anno_size, simple_anno_size_adjust = object@param$simple_anno_size_adjust)
object |
A |
annotation_height |
A vector of of annotation heights in |
annotation_width |
A vector of of annotation widths in |
height |
The height of the complete heatmap annotation. |
width |
The width of the complete heatmap annotation. |
simple_anno_size |
The size of one line of the simple annotation. |
simple_anno_size_adjust |
Whether adjust the size of the simple annotation? |
The function only adjust height for column annotations and width for row annotations.
The basic rules are (take height and annotation_height for example:
1. If annotation_height is set and all
annotation_height are absolute units, height is ignored.
2. If annotation_height contains non-absolute units, height also need to be set and the
non-absolute units should be set in a simple form such as 1:10 or unit(1, "null").
3. simple_anno_size is only used when annotation_height is NULL.
4. If only height is set, non-simple annotation is adjusted while keeps simple anntation unchanged.
5. If only height is set and all annotations are simple annotations, all anntations are adjusted,
and simple_anno_size is disabled.
6. If simple_anno_size_adjust is FALSE, the size of the simple annotations will not change.
# There is no example NULL# There is no example NULL
Restore the index vector to index matrix in layer_fun
restore_matrix(j, i, x, y)restore_matrix(j, i, x, y)
j |
Column indices directly from |
i |
Row indices directly from |
x |
Position on x-direction directly from |
y |
Position on y-direction directly from |
The values that are sent to layer_fun are all vectors (for the vectorization
of the grid graphic functions), however, the heatmap slice where
layer_fun is applied to, is still represented by a matrix, thus, it would be
very convinient if all the arguments in layer_fun can be converted to the
sub-matrix for the current slice. Here, as shown in above example,
restore_matrix does the job. restore_matrix directly accepts the first
four argument in layer_fun and returns an index matrix, where rows and
columns correspond to the rows and columns in the current slice, from top to
bottom and from left to right. The values in the matrix are the natural order
of e.g. vector j in current slice.
For following code:
Heatmap(small_mat, name = "mat", col = col_fun,
row_km = 2, column_km = 2,
layer_fun = function(j, i, x, y, w, h, fill) {
ind_mat = restore_matrix(j, i, x, y)
print(ind_mat)
}
)
The first output which is for the top-left slice:
[,1] [,2] [,3] [,4] [,5]
[1,] 1 4 7 10 13
[2,] 2 5 8 11 14
[3,] 3 6 9 12 15
As you see, this is a three-row and five-column index matrix where the first
row corresponds to the top row in the slice. The values in the matrix
correspond to the natural index (i.e. 1, 2, ...) in j, i, x, y,
... in layer_fun. Now, if we want to add values on the second column in the
top-left slice, the code which is put inside layer_fun would look like:
for(ind in ind_mat[, 2]) {
grid.text(small_mat[i[ind], j[ind]], x[ind], y[ind], ...)
}
set.seed(123) mat = matrix(rnorm(81), nr = 9) Heatmap(mat, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, width, height, fill) { ind_mat = restore_matrix(j, i, x, y) print(ind_mat) }) set.seed(123) mat = matrix(round(rnorm(81), 2), nr = 9) Heatmap(mat, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, width, height, fill) { ind_mat = restore_matrix(j, i, x, y) ind = unique(c(ind_mat[2, ], ind_mat[, 3])) grid.text(pindex(mat, i[ind], j[ind]), x[ind], y[ind]) })set.seed(123) mat = matrix(rnorm(81), nr = 9) Heatmap(mat, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, width, height, fill) { ind_mat = restore_matrix(j, i, x, y) print(ind_mat) }) set.seed(123) mat = matrix(round(rnorm(81), 2), nr = 9) Heatmap(mat, row_km = 2, column_km = 2, layer_fun = function(j, i, x, y, width, height, fill) { ind_mat = restore_matrix(j, i, x, y) ind = unique(c(ind_mat[2, ], ind_mat[, 3])) grid.text(pindex(mat, i[ind], j[ind]), x[ind], y[ind]) })
Barplots as Row Annotation
row_anno_barplot(...)row_anno_barplot(...)
... |
pass to |
A wrapper of anno_barplot with pre-defined which to row.
You can directly use anno_barplot for row annotation if you call it in rowAnnotation.
See help page of anno_barplot.
# There is no example NULL# There is no example NULL
Boxplots as Row Annotation
row_anno_boxplot(...)row_anno_boxplot(...)
... |
pass to |
A wrapper of anno_boxplot with pre-defined which to row.
You can directly use anno_boxplot for row annotation if you call it in rowAnnotation.
See help page of anno_boxplot.
# There is no example NULL# There is no example NULL
Density as Row Annotation
row_anno_density(...)row_anno_density(...)
... |
pass to |
A wrapper of anno_density with pre-defined which to row.
You can directly use anno_density for row annotation if you call it in rowAnnotation.
See help page of anno_density.
# There is no example NULL# There is no example NULL
Histograms as Row Annotation
row_anno_histogram(...)row_anno_histogram(...)
... |
pass to |
A wrapper of anno_histogram with pre-defined which to row.
You can directly use anno_histogram for row annotation if you call it in rowAnnotation.
See help page of anno_histogram.
# There is no example NULL# There is no example NULL
Points as Row Annotation
row_anno_points(...)row_anno_points(...)
... |
pass to |
A wrapper of anno_points with pre-defined which to row.
You can directly use anno_points for row annotation if you call it in rowAnnotation.
See help page of anno_points.
# There is no example NULL# There is no example NULL
Text as Row Annotation
row_anno_text(...)row_anno_text(...)
... |
pass to |
A wrapper of anno_text with pre-defined which to row.
You can directly use anno_text for row annotation if you call it in rowAnnotation.
See help page of anno_text.
# There is no example NULL# There is no example NULL
Method dispatch page for row_dend.
row_dend can be dispatched on following classes:
row_dend,HeatmapList-method, HeatmapList-class class method
row_dend,Heatmap-method, Heatmap-class class method
# no example NULL# no example NULL
Get Row Dendrograms from a Heatmap
## S4 method for signature 'Heatmap' row_dend(object, on_slice = FALSE)## S4 method for signature 'Heatmap' row_dend(object, on_slice = FALSE)
object |
A |
on_slice |
If the value is TRUE, it returns the dendrogram on the slice level. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) row_dend(ht) ht = Heatmap(mat, row_km = 2) ht = draw(ht) row_dend(ht)mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) row_dend(ht) ht = Heatmap(mat, row_km = 2) ht = draw(ht) row_dend(ht)
Get Row Dendrograms from a Heatmap List
## S4 method for signature 'HeatmapList' row_dend(object, name = NULL, on_slice = FALSE)## S4 method for signature 'HeatmapList' row_dend(object, name = NULL, on_slice = FALSE)
object |
A |
name |
Name of a specific heatmap. |
on_slice |
If the value is TRUE, it returns the dendrogram on the slice level. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list) ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list) row_dend(ht_list, on_slice = TRUE) ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list)mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list) ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list) row_dend(ht_list, on_slice = TRUE) ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) row_dend(ht_list)
Method dispatch page for row_order.
row_order can be dispatched on following classes:
row_order,HeatmapList-method, HeatmapList-class class method
row_order,Heatmap-method, Heatmap-class class method
# no example NULL# no example NULL
Get Row Order from a Heatmap
## S4 method for signature 'Heatmap' row_order(object)## S4 method for signature 'Heatmap' row_order(object)
object |
A |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) row_order(ht) ht = Heatmap(mat, row_km = 2) ht = draw(ht) row_order(ht)mat = matrix(rnorm(100), 10) ht = Heatmap(mat) ht = draw(ht) row_order(ht) ht = Heatmap(mat, row_km = 2) ht = draw(ht) row_order(ht)
Get Row Order from a Heatmap List
## S4 method for signature 'HeatmapList' row_order(object, name = NULL)## S4 method for signature 'HeatmapList' row_order(object, name = NULL)
object |
A |
name |
Name of a specific heatmap. |
The format of the returned object depends on whether rows/columns of the heatmaps are split.
Zuguang Gu <[email protected]>
mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list) ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list) ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list)mat = matrix(rnorm(100), 10) ht_list = Heatmap(mat) + Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list) ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list) ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat) ht_list = draw(ht_list) row_order(ht_list)
Construct Row Annotations
rowAnnotation(...)rowAnnotation(...)
... |
Pass to |
The function is identical to
HeatmapAnnotation(..., which = "row")
A HeatmapAnnotation-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Set Height of Heatmap Component
## S4 method for signature 'Heatmap' set_component_height(object, k, v)## S4 method for signature 'Heatmap' set_component_height(object, k, v)
object |
A |
k |
Which column component? The value should a numeric index or the name of the corresponding column component. See **Detials**. |
v |
Height of the component, a |
All column components are: column_title_top, column_dend_top, column_names_top,
column_anno_top, heatmap_body, column_anno_bottom, column_names_bottom,
column_dend_bottom, column_title_bottom.
This function is only for internal use.
The Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Set Width of Heatmap Component
## S4 method for signature 'Heatmap' set_component_width(object, k, v)## S4 method for signature 'Heatmap' set_component_width(object, k, v)
object |
A |
k |
Which row component? The value should a numeric index or the name of the corresponding row component. See **Detials**. |
v |
width of the component, a |
All row components are: row_title_left, row_dend_left, row_names_left, row_anno_left,
heatmap_body, row_anno_right, row_names_right, row_dend_right, row_title_right.
This function is only for internal use.
The Heatmap-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Set Names
set_name(m)set_name(m)
m |
A combination matrix returned by |
A vector of set names.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_name(m)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_name(m)
Modify Set Names
set_name(x, ...) <- valueset_name(x, ...) <- value
x |
A combination matrix returned by |
value |
New set names. |
... |
Other arguments. |
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_name(m) = c("A", "B", "C") mset.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_name(m) = c("A", "B", "C") m
Set Sizes
set_size(m)set_size(m)
m |
A combination matrix returned by |
A vector of set sizes.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_size(m)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) set_size(m)
Print the AnnotationFunction Object
## S4 method for signature 'AnnotationFunction' show(object)## S4 method for signature 'AnnotationFunction' show(object)
object |
The |
# There is no example NULL# There is no example NULL
Print the ColorMapping Object
## S4 method for signature 'ColorMapping' show(object)## S4 method for signature 'ColorMapping' show(object)
object |
A |
This function returns no value.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Method dispatch page for show.
show can be dispatched on following classes:
show,AnnotationFunction-method, AnnotationFunction-class class method
show,Heatmap-method, Heatmap-class class method
show,HeatmapList-method, HeatmapList-class class method
show,ColorMapping-method, ColorMapping-class class method
show,HeatmapAnnotation-method, HeatmapAnnotation-class class method
show,SingleAnnotation-method, SingleAnnotation-class class method
# no example NULL# no example NULL
Draw the Single Heatmap with Defaults
## S4 method for signature 'Heatmap' show(object)## S4 method for signature 'Heatmap' show(object)
object |
A |
It actually calls draw,Heatmap-method, but only with default parameters. If users want to customize the heatmap,
they can pass parameters directly to draw,Heatmap-method.
The HeatmapList-class object.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Print the HeatmapAnnotation object
## S4 method for signature 'HeatmapAnnotation' show(object)## S4 method for signature 'HeatmapAnnotation' show(object)
object |
A |
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Draw a list of heatmaps with default parameters
## S4 method for signature 'HeatmapList' show(object)## S4 method for signature 'HeatmapList' show(object)
object |
a |
Actually it calls draw,HeatmapList-method, but only with default parameters. If users want to customize the heatmap,
they can pass parameters directly to draw,HeatmapList-method.
This function returns no value.
# There is no example NULL# There is no example NULL
Print the SingleAnnotation object
## S4 method for signature 'SingleAnnotation' show(object)## S4 method for signature 'SingleAnnotation' show(object)
object |
A |
No value is returned.
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Constructor Method for SingleAnnotation Class
SingleAnnotation(name, value, col, fun, label = NULL, na_col = "grey", which = c("column", "row"), show_legend = TRUE, gp = gpar(col = NA), border = FALSE, legend_param = list(), show_name = TRUE, name_gp = gpar(fontsize = 12), name_offset = NULL, name_side = ifelse(which == "column", "right", "bottom"), name_rot = NULL, simple_anno_size = ht_opt$simple_anno_size, width = NULL, height = NULL)SingleAnnotation(name, value, col, fun, label = NULL, na_col = "grey", which = c("column", "row"), show_legend = TRUE, gp = gpar(col = NA), border = FALSE, legend_param = list(), show_name = TRUE, name_gp = gpar(fontsize = 12), name_offset = NULL, name_side = ifelse(which == "column", "right", "bottom"), name_rot = NULL, simple_anno_size = ht_opt$simple_anno_size, width = NULL, height = NULL)
name |
Name for the annotation. If it is not specified, an internal name is assigned. |
value |
A vector or a matrix of discrete or continuous values. |
col |
Colors corresponding to |
fun |
A user-defined function to add annotation graphics. The argument of this function should be at least a vector of index that corresponds to rows or columns. Normally the function should be constructed by |
label |
Label for the annotation. By default is the annotation name. |
na_col |
Color for |
which |
Whether the annotation is a row annotation or a column annotation? |
show_legend |
If it is a simple annotation, whether show legend in the final heatmap? |
gp |
Since simple annotation is represented as rows of grids. This argument controls graphic parameters for the simple annotation. The |
border |
border, only work for simple annotation |
legend_param |
Parameters for the legend. See |
show_name |
Whether show annotation name? |
name_gp |
Graphic parameters for annotation name. |
name_offset |
Offset to the annotation, a |
name_side |
'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations |
name_rot |
Rotation of the annotation name. |
simple_anno_size |
size of the simple annotation. |
width |
The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit. |
height |
The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit. |
A single annotation is a basic unit of complex heatmap annotations where the heamtap annotations are always a list of single annotations. An annotation can be simply heatmap-like (here we call it simple annotation) or more complex like points, lines, boxes (for which we call it complex annotation).
In the SingleAnnotation constructor, value, col, na_col are used to construct a anno_simple
annotation funciton which is generated internally by AnnotationFunction. The legend of the simple annotation
can be automatcally generated,
For construcing a complex annotation, users need to use fun which is a user-defind function. Normally it
is constucted by AnnotationFunction. One big advantage for using AnnotationFunction is the annotation function
or the graphics drawn by the annotation function can be split according to row splitting or column splitting of
the heatmap. Users can also provide a "pure" function which is a normal R function for the fun argument.
The function only needs one argument which is a vector of index for rows or columns depending whether it is
a row annotation or column annotation. The other two optional arguments are the current slice index and total
number of slices. See **Examples** section for an example. If it is a normal R function, it will be constructed
into the AnnotationFunction-class object internally.
The SingleAnnotation-class is a simple wrapper on top of AnnotationFunction-class only with annotation
name added.
The class also stored the "extended area" relative to the area for the annotation graphics. The extended areas are those created by annotation names and axes.
A SingleAnnotation-class object.
Zuguang Gu <[email protected]>
There are following built-in annotation functions that can be directly used to generate complex annotations:
anno_simple, anno_points, anno_lines, anno_barplot, anno_histogram, anno_boxplot, anno_density, anno_text,
anno_joyplot, anno_horizon, anno_image, anno_block, anno_summary and anno_mark.
ha = SingleAnnotation(value = 1:10) draw(ha, test = "single column annotation") m = cbind(1:10, 10:1) colnames(m) = c("a", "b") ha = SingleAnnotation(value = m) draw(ha, test = "matrix as column annotation") anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1))) ha = SingleAnnotation(fun = anno) draw(ha, test = "anno_barplot as input") fun = local({ # because there variables outside the function for use, we put it a local environment value = 1:10 function(index, k = 1, n = 1) { pushViewport(viewport(xscale = c(0.5, length(index) + 0.5), yscale = range(value))) grid.points(seq_along(index), value[index]) grid.rect() if(k == 1) grid.yaxis() popViewport() } }) ha = SingleAnnotation(fun = fun, height = unit(4, "cm")) draw(ha, index = 1:10, test = "self-defined function")ha = SingleAnnotation(value = 1:10) draw(ha, test = "single column annotation") m = cbind(1:10, 10:1) colnames(m) = c("a", "b") ha = SingleAnnotation(value = m) draw(ha, test = "matrix as column annotation") anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1))) ha = SingleAnnotation(fun = anno) draw(ha, test = "anno_barplot as input") fun = local({ # because there variables outside the function for use, we put it a local environment value = 1:10 function(index, k = 1, n = 1) { pushViewport(viewport(xscale = c(0.5, length(index) + 0.5), yscale = range(value))) grid.points(seq_along(index), value[index]) grid.rect() if(k == 1) grid.yaxis() popViewport() } }) ha = SingleAnnotation(fun = fun, height = unit(4, "cm")) draw(ha, index = 1:10, test = "self-defined function")
Class for a Single Annotation
The SingleAnnotation-class is used for storing data for a single annotation and provides
methods for drawing annotation graphics.
The SingleAnnotation-class provides following methods:
SingleAnnotation: constructor method
draw,SingleAnnotation-method: draw the single annotation.
Zuguang Gu <[email protected]>
The SingleAnnotation-class is always used internally. The public HeatmapAnnotation-class
contains a list of SingleAnnotation-class objects and is used to add annotation graphics on heatmaps.
# There is no example NULL# There is no example NULL
Size of the AnnotationFunction Object
## S3 method for class 'AnnotationFunction' size(x, ...)## S3 method for class 'AnnotationFunction' size(x, ...)
x |
The |
... |
Other arguments. |
It returns the width if it is a row annotation and the height if it is a column annotation.
Internally used.
anno = anno_points(1:10) ComplexHeatmap:::size(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::size(anno)anno = anno_points(1:10) ComplexHeatmap:::size(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::size(anno)
Size of the HeatmapAnnotation Object
## S3 method for class 'HeatmapAnnotation' size(x, ...)## S3 method for class 'HeatmapAnnotation' size(x, ...)
x |
The |
... |
Other arguments. |
It returns the width if it is a row annotation and the height if it is a column annotation.
Internally used.
# There is no example NULL# There is no example NULL
Size of the SingleAnnotation Object
## S3 method for class 'SingleAnnotation' size(x, ...)## S3 method for class 'SingleAnnotation' size(x, ...)
x |
The |
... |
Other arguments. |
It returns the width if it is a row annotation and the height if it is a column annotation.
Internally used.
# There is no example NULL# There is no example NULL
Assign the Size to the AnnotationFunction Object
## S3 replacement method for class 'AnnotationFunction' size(x, ...) <- value## S3 replacement method for class 'AnnotationFunction' size(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
It assigns to the width if it is a row annotation and the height if it is a column annotation.
Internally used.
anno = anno_points(1:10) ComplexHeatmap:::size(anno) = unit(4, "cm") ComplexHeatmap:::size(anno)anno = anno_points(1:10) ComplexHeatmap:::size(anno) = unit(4, "cm") ComplexHeatmap:::size(anno)
Assign the Size to the HeatmapAnnotation Object
## S3 replacement method for class 'HeatmapAnnotation' size(x, ...) <- value## S3 replacement method for class 'HeatmapAnnotation' size(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
It assigns the width if it is a row annotation and the height if it is a column annotation.
Internally used.
# There is no example NULL# There is no example NULL
Assign the Size to the SingleAnnotation Object
## S3 replacement method for class 'SingleAnnotation' size(x, ...) <- value## S3 replacement method for class 'SingleAnnotation' size(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
It assigns to the width if it is a row annotation and the height if it is a column annotation.
Internally used.
# There is no example NULL# There is no example NULL
Adjust positions of rectanglar shapes
smartAlign2(start, end, range, plot = FALSE)smartAlign2(start, end, range, plot = FALSE)
start |
position which corresponds to the start (bottom or left) of the rectangle-shapes. |
end |
position which corresponds to the end (top or right) of the rectanglar shapes. |
range |
data ranges (the minimal and maximal values) |
plot |
Whether plot the correspondance between the original positions and the adjusted positions. Only for testing. |
This is an improved version of the smartAlign.
It adjusts the positions of the rectangular shapes to make them do not overlap
range = c(0, 10) pos1 = rbind(c(1, 2), c(5, 7)) smartAlign2(pos1, range = range, plot = TRUE) range = c(0, 10) pos1 = rbind(c(-0.5, 2), c(5, 7)) smartAlign2(pos1, range = range, plot = TRUE) pos1 = rbind(c(-1, 2), c(3, 4), c(5, 6), c(7, 11)) pos1 = pos1 + runif(length(pos1), max = 0.3, min = -0.3) omfrow = par("mfrow") par(mfrow = c(3, 3)) for(i in 1:9) { ind = sample(4, 4) smartAlign2(pos1[ind, ], range = range, plot = TRUE) } par(mfrow = omfrow) pos1 = rbind(c(3, 6), c(4, 7)) smartAlign2(pos1, range = range, plot = TRUE) pos1 = rbind(c(1, 8), c(3, 10)) smartAlign2(pos1, range = range, plot = TRUE)range = c(0, 10) pos1 = rbind(c(1, 2), c(5, 7)) smartAlign2(pos1, range = range, plot = TRUE) range = c(0, 10) pos1 = rbind(c(-0.5, 2), c(5, 7)) smartAlign2(pos1, range = range, plot = TRUE) pos1 = rbind(c(-1, 2), c(3, 4), c(5, 6), c(7, 11)) pos1 = pos1 + runif(length(pos1), max = 0.3, min = -0.3) omfrow = par("mfrow") par(mfrow = c(3, 3)) for(i in 1:9) { ind = sample(4, 4) smartAlign2(pos1[ind, ], range = range, plot = TRUE) } par(mfrow = omfrow) pos1 = rbind(c(3, 6), c(4, 7)) smartAlign2(pos1, range = range, plot = TRUE) pos1 = rbind(c(1, 8), c(3, 10)) smartAlign2(pos1, range = range, plot = TRUE)
str method
## S3 method for class 'comb_mat' str(object, ...)## S3 method for class 'comb_mat' str(object, ...)
object |
A combination matrix returned by |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Subset a gpar Object
subset_gp(gp, i)subset_gp(gp, i)
gp |
A |
i |
A vector of indices. |
A gpar object.
gp = gpar(col = 1:10, fill = 1) subset_gp(gp, 1:5)gp = gpar(col = 1:10, fill = 1) subset_gp(gp, 1:5)
Subset the Matrix by Rows
subset_matrix_by_row(x, i)subset_matrix_by_row(x, i)
x |
A matrix. |
i |
The row indices. |
Mainly used for constructing the AnnotationFunction-class object.
# There is no example NULL# There is no example NULL
Do not do subseting
subset_no(x, i)subset_no(x, i)
x |
A vector. |
i |
The indices. |
Mainly used for constructing the AnnotationFunction-class object.
# There is no example NULL# There is no example NULL
Subset the vector
subset_vector(x, i)subset_vector(x, i)
x |
A vector. |
i |
The indices. |
Mainly used for constructing the AnnotationFunction-class object.
# There is no example NULL# There is no example NULL
Print the Summary of a Heatmap
## S3 method for class 'Heatmap' summary(object, ...)## S3 method for class 'Heatmap' summary(object, ...)
object |
A |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Summary of a Heatmap List
## S3 method for class 'HeatmapList' summary(object, ...)## S3 method for class 'HeatmapList' summary(object, ...)
object |
A |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Transpost the Combination Matrix
## S3 method for class 'comb_mat' t(x)## S3 method for class 'comb_mat' t(x)
x |
A combination matrix returned by |
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) t(m)set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) t(m)
Test alter_fun for oncoPrint()
test_alter_fun(fun, type, asp_ratio = 1)test_alter_fun(fun, type, asp_ratio = 1)
fun |
The |
type |
A vector of alteration types. It is only used when |
asp_ratio |
The aspect ratio (width/height) for the small rectangles. |
This function helps you to have a quick view of how the graphics for each alteration type and combinations look like.
alter_fun = list( mut1 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "red", col = NA)), mut2 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "blue", col = NA)), mut3 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "yellow", col = NA)), mut4 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "purple", col = NA)), mut5 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(lwd = 2)), mut6 = function(x, y, w, h) grid.points(x, y, pch = 16), mut7 = function(x, y, w, h) grid.segments(x - w*0.5, y - h*0.5, x + w*0.5, y + h*0.5, gp = gpar(lwd = 2)) ) test_alter_fun(alter_fun)alter_fun = list( mut1 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "red", col = NA)), mut2 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "blue", col = NA)), mut3 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "yellow", col = NA)), mut4 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "purple", col = NA)), mut5 = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(lwd = 2)), mut6 = function(x, y, w, h) grid.points(x, y, pch = 16), mut7 = function(x, y, w, h) grid.segments(x - w*0.5, y - h*0.5, x + w*0.5, y + h*0.5, gp = gpar(lwd = 2)) ) test_alter_fun(alter_fun)
A simple grob for the word cloud
textbox_grob(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", gp = gpar(), background_gp = gpar(col = "black", fill = "transparent"), round_corners = FALSE, r = unit(0.1, "snpc"), line_space = unit(4, "pt"), text_space = unit(4, "pt"), max_width = unit(100, "mm"), padding = unit(4, "pt"), first_text_from = "top", add_new_line = FALSE, word_wrap = FALSE)textbox_grob(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", gp = gpar(), background_gp = gpar(col = "black", fill = "transparent"), round_corners = FALSE, r = unit(0.1, "snpc"), line_space = unit(4, "pt"), text_space = unit(4, "pt"), max_width = unit(100, "mm"), padding = unit(4, "pt"), first_text_from = "top", add_new_line = FALSE, word_wrap = FALSE)
text |
A vector of texts. The value can be single words or phrases/sentenses. |
x |
X position. |
y |
Y position. |
just |
Justification of the box in the viewport. |
gp |
Graphics parameters of texts. |
background_gp |
Graphics parameters for the box. |
round_corners |
Whether to draw round corners for the box. |
r |
Radius of the round corners. |
line_space |
Space between lines. The value can be a |
text_space |
Space between texts The value can be a |
max_width |
The maximal width of the viewport to put the word cloud. The value can be a |
padding |
Padding of the box, i.e. space between text and the four box borders. The value should be a |
first_text_from |
Should the texts be added from the top of the box or from the bottom? Value should be either "top" or "bottom". |
add_new_line |
Whether to add new line after every text? If |
word_wrap |
Whether to apply word wrap for phrases/sentenses. |
A grob object. The width and height of the grob can be get by grobWidth and grobHeight.
words = sapply(1:30, function(x) strrep(sample(letters, 1), sample(3:10, 1))) grid.newpage() grid.textbox(words, gp = gpar(fontsize = runif(30, min = 5, max = 30))) sentenses = c("This is sentense 1", "This is a long long long long long long long sentense.") grid.newpage() grid.textbox(sentenses) grid.textbox(sentenses, word_wrap = TRUE) grid.textbox(sentenses, word_wrap = TRUE, add_new_line = TRUE)words = sapply(1:30, function(x) strrep(sample(letters, 1), sample(3:10, 1))) grid.newpage() grid.textbox(words, gp = gpar(fontsize = runif(30, min = 5, max = 30))) sentenses = c("This is sentense 1", "This is a long long long long long long long sentense.") grid.newpage() grid.textbox(sentenses) grid.textbox(sentenses, word_wrap = TRUE) grid.textbox(sentenses, word_wrap = TRUE, add_new_line = TRUE)
Unify a List of Matrix
unify_mat_list(mat_list, default = 0)unify_mat_list(mat_list, default = 0)
mat_list |
A list of matrix. All of them should have dimension names. |
default |
Default values for the newly added rows and columns. |
All matrix will be unified to have same row names and column names.
A list of matrix
Zuguang Gu <[email protected]>
# There is no example NULL# There is no example NULL
Make the UpSet plot
UpSet(m, comb_col = "black", pt_size = unit(3, "mm"), lwd = 2, bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC", set_order = order(set_size(m), decreasing = TRUE), comb_order = if(attr(m, "param")$set_on_rows) { order.comb_mat(m[set_order, ], decreasing = TRUE) } else { order.comb_mat(m[, set_order], decreasing = TRUE) }, top_annotation = upset_top_annotation(m), right_annotation = upset_right_annotation(m), left_annotation = NULL, row_names_side = "left", ...)UpSet(m, comb_col = "black", pt_size = unit(3, "mm"), lwd = 2, bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC", set_order = order(set_size(m), decreasing = TRUE), comb_order = if(attr(m, "param")$set_on_rows) { order.comb_mat(m[set_order, ], decreasing = TRUE) } else { order.comb_mat(m[, set_order], decreasing = TRUE) }, top_annotation = upset_top_annotation(m), right_annotation = upset_right_annotation(m), left_annotation = NULL, row_names_side = "left", ...)
m |
A combination matrix returned by |
comb_col |
The color for the dots representing combination sets. |
pt_size |
The point size for the dots representing combination sets. |
lwd |
The line width for the combination sets. |
bg_col |
Color for the background rectangles. |
bg_pt_col |
Color for the dots representing the set is not selected. |
set_order |
The order of sets. |
comb_order |
The order of combination sets. |
top_annotation |
A |
left_annotation |
A |
right_annotation |
A |
row_names_side |
The side of row names. |
... |
Other arguments passed to |
By default, the sets are on rows and combination sets are on columns. The positions of the two types of sets can be switched by transposing the matrix.
When sets are on rows, the default top annotation is the barplot showing the size of each
combination sets and the default right annotation is the barplot showing the size of the sets.
The annotations are simply constructed by HeatmapAnnotation and anno_barplot with some
parameters pre-set. Users can check the source code of upset_top_annotation and
upset_right_annotation to find out how the annotations are defined.
To change or to add annotations, users just need to define a new HeatmapAnnotation object.
E.g. if we want to change the side of the axis and name on top annotation:
Upset(..., top_annotation =
HeatmapAnnotation(
"Intersection size" = anno_barplot(
comb_size(m),
border = FALSE,
gp = gpar(fill = "black"),
height = unit(2, "cm"),
axis_param = list(side = "right")
),
annotation_name_side = "right",
annotation_name_rot = 0)
)
To add more annotations on top, users just add it in HeatmapAnnotation:
Upset(..., top_annotation =
HeatmapAnnotation(
"Intersection size" = anno_barplot(
comb_size(m),
border = FALSE,
gp = gpar(fill = "black"),
height = unit(2, "cm"),
axis_param = list(side = "right")
),
"anno1" = anno_points(...),
"anno2" = some_vector,
annotation_name_side = "right",
annotation_name_rot = 0)
)
And so is for the right annotations.
UpSet returns a Heatmap-class object, which means, you can add it with other heatmaps and annotations
by + or %v%.
set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) UpSet(m) UpSet(t(m)) m = make_comb_mat(lt, mode = "union") UpSet(m) UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1)) # compare two UpSet plots set.seed(123) lt1 = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m1 = make_comb_mat(lt1) set.seed(456) lt2 = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m2 = make_comb_mat(lt2) max1 = max(c(set_size(m1), set_size(m2))) max2 = max(c(comb_size(m1), comb_size(m2))) UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)), right_annotation = upset_right_annotation(m1, ylim = c(0, max1)), column_title = "UpSet1") + UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)), right_annotation = upset_right_annotation(m2, ylim = c(0, max1)), column_title = "UpSet2")set.seed(123) lt = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m = make_comb_mat(lt) UpSet(m) UpSet(t(m)) m = make_comb_mat(lt, mode = "union") UpSet(m) UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1)) # compare two UpSet plots set.seed(123) lt1 = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m1 = make_comb_mat(lt1) set.seed(456) lt2 = list(a = sample(letters, 10), b = sample(letters, 15), c = sample(letters, 20)) m2 = make_comb_mat(lt2) max1 = max(c(set_size(m1), set_size(m2))) max2 = max(c(comb_size(m1), comb_size(m2))) UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)), right_annotation = upset_right_annotation(m1, ylim = c(0, max1)), column_title = "UpSet1") + UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)), right_annotation = upset_right_annotation(m2, ylim = c(0, max1)), column_title = "UpSet2")
UpSet Left Annotation
upset_left_annotation(m, gp = gpar(fill = "black"), axis_param = list(direction = "reverse"), width = unit(ifelse(set_on_rows, 2, 3), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "bottom", annotation_name_rot = NULL, ...)upset_left_annotation(m, gp = gpar(fill = "black"), axis_param = list(direction = "reverse"), width = unit(ifelse(set_on_rows, 2, 3), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "bottom", annotation_name_rot = NULL, ...)
m |
A combination matrix which is as same as the one for |
gp |
Graphic parameters for bars. |
axis_param |
Parameters for axis. |
width |
Width of the left annotation. |
show_annotation_name |
Whether show annotation names? |
annotation_name_gp |
Graphic parameters for anntation names. |
annotation_name_offset |
Offset to the annotation name, a |
annotation_name_side |
Side of the annotation name. |
annotation_name_rot |
Rotation of the annotation name, it can only take values in |
... |
Passed to |
# There is no example NULL# There is no example NULL
Default UpSet Right Annotation
upset_right_annotation(m, gp = gpar(fill = "black"), width = unit(ifelse(set_on_rows, 2, 3), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "bottom", annotation_name_rot = NULL, ...)upset_right_annotation(m, gp = gpar(fill = "black"), width = unit(ifelse(set_on_rows, 2, 3), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "bottom", annotation_name_rot = NULL, ...)
m |
A combination matrix which is as same as the one for |
gp |
Graphic parameters for bars. |
width |
Width of the right annotation. |
show_annotation_name |
Whether show annotation names? |
annotation_name_gp |
Graphic parameters for anntation names. |
annotation_name_offset |
Offset to the annotation name, a |
annotation_name_side |
Side of the annotation name. |
annotation_name_rot |
Rotation of the annotation name, it can only take values in |
... |
Passed to |
The default right annotation is actually barplot implemented by anno_barplot. For
how to set the right annotation or left annotation in UpSet, please refer to UpSet.
If you want to use decorate_annotation function, the annotation name for the "sets"
is set_size and the annotation name for the "intersection sets" are intersection_size
and if under the union mode, it is union_size.
# There is no example NULL# There is no example NULL
Default UpSet Top Annotation
upset_top_annotation(m, gp = gpar(fill = "black"), height = unit(ifelse(set_on_rows, 3, 2), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "left", annotation_name_rot = 0, ...)upset_top_annotation(m, gp = gpar(fill = "black"), height = unit(ifelse(set_on_rows, 3, 2), "cm"), show_annotation_name = TRUE, annotation_name_gp = gpar(), annotation_name_offset = NULL, annotation_name_side = "left", annotation_name_rot = 0, ...)
m |
A combination matrix which is as same as the one for |
gp |
Graphic parameters for bars. |
height |
The height of the top annotation. |
show_annotation_name |
Whether show annotation names? |
annotation_name_gp |
Graphic parameters for anntation names. |
annotation_name_offset |
Offset to the annotation name, a |
annotation_name_side |
Side of the annotation name. |
annotation_name_rot |
Rotation of the annotation name, it can only take values in |
... |
Passed to |
The default top annotation is actually barplot implemented by anno_barplot. For
how to set the top annotation or bottom annotation in UpSet, please refer to UpSet.
If you want to use decorate_annotation function, the annotation name for the "sets"
is set_size and the annotation name for the "intersection sets" are intersection_size
and if under the union mode, it is union_size.
# There is no example NULL# There is no example NULL
Width of the AnnotationFunction Object
## S3 method for class 'AnnotationFunction' width(x, ...)## S3 method for class 'AnnotationFunction' width(x, ...)
x |
A |
... |
Other arguments. |
Internally used.
anno = anno_points(1:10) ComplexHeatmap:::width(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::width(anno)anno = anno_points(1:10) ComplexHeatmap:::width(anno) anno = anno_points(1:10, which = "row") ComplexHeatmap:::width(anno)
Width of the Heatmap
## S3 method for class 'Heatmap' width(x, ...)## S3 method for class 'Heatmap' width(x, ...)
x |
The |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Width of the HeatmapAnnotation Object
## S3 method for class 'HeatmapAnnotation' width(x, ...)## S3 method for class 'HeatmapAnnotation' width(x, ...)
x |
The |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Width of the Heatmap List
## S3 method for class 'HeatmapList' width(x, ...)## S3 method for class 'HeatmapList' width(x, ...)
x |
The |
... |
Other arguments. |
# There is no example NULL# There is no example NULL
Width of the Legends
## S3 method for class 'Legends' width(x, ...)## S3 method for class 'Legends' width(x, ...)
x |
The |
... |
Other arguments. |
The returned unit x is always in mm.
lgd = Legend(labels = 1:10, title = "foo", legend_gp = gpar(fill = "red")) ComplexHeatmap:::width(lgd)lgd = Legend(labels = 1:10, title = "foo", legend_gp = gpar(fill = "red")) ComplexHeatmap:::width(lgd)
Width of the SingleAnnotation Object
## S3 method for class 'SingleAnnotation' width(x, ...)## S3 method for class 'SingleAnnotation' width(x, ...)
x |
The |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Width to the AnnotationFunction Object
## S3 replacement method for class 'AnnotationFunction' width(x, ...) <- value## S3 replacement method for class 'AnnotationFunction' width(x, ...) <- value
x |
The |
... |
Other arguments. |
value |
A |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Width to the HeatmapAnnotation Object
## S3 replacement method for class 'HeatmapAnnotation' width(x, ...) <- value## S3 replacement method for class 'HeatmapAnnotation' width(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Assign the Width to the SingleAnnotation Object
## S3 replacement method for class 'SingleAnnotation' width(x, ...) <- value## S3 replacement method for class 'SingleAnnotation' width(x, ...) <- value
x |
The |
value |
A |
... |
Other arguments. |
Internally used.
# There is no example NULL# There is no example NULL
Width for annotation_axis Grob
## S3 method for class 'annotation_axis' widthDetails(x)## S3 method for class 'annotation_axis' widthDetails(x)
x |
The |
The physical width of the grob can be get by convertWidth(grobWidth(axis_grob), "mm").
# There is no example NULL# There is no example NULL
Grob width for packed_legends
## S3 method for class 'legend' widthDetails(x)## S3 method for class 'legend' widthDetails(x)
x |
A legend object. |
# There is no example NULL# There is no example NULL
Grob width for legend_body
## S3 method for class 'legend_body' widthDetails(x)## S3 method for class 'legend_body' widthDetails(x)
x |
A legend_body object. |
# There is no example NULL# There is no example NULL
Grob width for packed_legends
## S3 method for class 'packed_legends' widthDetails(x)## S3 method for class 'packed_legends' widthDetails(x)
x |
A packed_legends object. |
# There is no example NULL# There is no example NULL
Width for textbox grob
## S3 method for class 'textbox' widthDetails(x)## S3 method for class 'textbox' widthDetails(x)
x |
The |
A unit object.
# There is no example NULL# There is no example NULL