Package 'gtrellis' reference manual

Title:	Genome Level Trellis Layout
Description:	Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.
Authors:	Zuguang Gu [aut, cre]
Maintainer:	Zuguang Gu <[email protected]>
License:	MIT + file LICENSE
Version:	1.39.0
Built:	2024-11-08 06:01:20 UTC
Source:	https://github.com/bioc/gtrellis

add heatmap to a new track

Description

add heatmap to a new track

Usage

add_heatmap_track(gr, mat, fill, border = NA, track = current_track() + 1, ...)
add_heatmap_track(gr, mat, fill, border = NA, track = current_track() + 1, ...)

Arguments

`gr`	genomic regions, it can be a data frame or a `GRanges` object
`mat`	matrix in which rows correspond to intervals in `gr`
`fill`	a color mapping function which maps values to colors. Users can consider `colorRamp2` to generate a color mapping function.
`border`	border of the grids in heatmap
`track`	which track the graphics will be added to. By default it is the next track. The value should only be a scalar.
`...`	other arguments passed to `add_track`

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

require(circlize)
bed = generateRandomBed(200)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
gtrellis_layout(nrow = 3, byrow = FALSE, track_axis = FALSE)
mat = matrix(rnorm(nrow(bed)*4), ncol = 4)
add_heatmap_track(bed, mat, fill = col_fun)
require(circlize)
bed = generateRandomBed(200)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
gtrellis_layout(nrow = 3, byrow = FALSE, track_axis = FALSE)
mat = matrix(rnorm(nrow(bed)*4), ncol = 4)
add_heatmap_track(bed, mat, fill = col_fun)

Add ideogram track

Description

Add ideogram track

Usage

add_ideogram_track(cytoband = system.file("extdata", "cytoBand.txt",
    package = "circlize"), species = NULL, track = current_track() + 1)
add_ideogram_track(cytoband = system.file("extdata", "cytoBand.txt",
    package = "circlize"), species = NULL, track = current_track() + 1)

Arguments

`cytoband`	Path of the cytoband file or a data frame that already contains cytoband data. Pass to `read.cytoband`.
`species`	Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download `cytoBand.txt.gz` from UCSC ftp automatically. Pass to `read.cytoband`.
`track`	which track the ideogram is added in. By default it is the next track in the layout.

Details

A track which contains ideograms will be added to the plot.

The function tries to download cytoband file from UCSC ftp. If there is no cytoband file available for the species, there will be an error.

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

add lines to a new or exsited track

Description

add lines to a new or exsited track

Usage

add_lines_track(gr, value, area = FALSE, baseline = "bottom", gp = gpar(), ...)
add_lines_track(gr, value, area = FALSE, baseline = "bottom", gp = gpar(), ...)

Arguments

`gr`	genomic regions, it can be a data frame or a `GRanges` object
`value`	numeric values associated with `gr`
`area`	whether draw polygon for the area under the line
`baseline`	baseline for drawing polygon
`gp`	graphic settings, should be specified by `gpar`.
`...`	other arguments passed to `add_track`

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

require(circlize)
bed = generateRandomBed(200)
gtrellis_layout(n_track = 2, track_ylim = rep(range(bed[[4]]), 2), nrow = 3, byrow = FALSE)
add_lines_track(bed, bed[[4]])
add_lines_track(bed, bed[[4]], area = TRUE, gp = gpar(fill = "grey", col = NA))
require(circlize)
bed = generateRandomBed(200)
gtrellis_layout(n_track = 2, track_ylim = rep(range(bed[[4]]), 2), nrow = 3, byrow = FALSE)
add_lines_track(bed, bed[[4]])
add_lines_track(bed, bed[[4]], area = TRUE, gp = gpar(fill = "grey", col = NA))

add points to a new or exsited track

Description

add points to a new or exsited track

Usage

add_points_track(gr, value, pch = 16, size = unit(1, "mm"), gp = gpar(), ...)
add_points_track(gr, value, pch = 16, size = unit(1, "mm"), gp = gpar(), ...)

Arguments

`gr`	genomic regions, it can be a data frame or a `GRanges` object
`value`	numeric values associated with `gr`
`pch`	shape of points
`size`	size of points, should be a `unit` object
`gp`	graphic settings, should be specified by `gpar`.
`...`	other arguments passed to `add_track`

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

require(circlize)
bed = generateRandomBed()
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_points_track(bed, bed[[4]], gp = gpar(col = ifelse(bed[[4]] > 0, "red", "green")))
require(circlize)
bed = generateRandomBed()
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_points_track(bed, bed[[4]], gp = gpar(col = ifelse(bed[[4]] > 0, "red", "green")))

add retangles to a new or exsited track

Description

add retangles to a new or exsited track

Usage

add_rect_track(gr, h1, h2, gp = gpar(), ...)
add_rect_track(gr, h1, h2, gp = gpar(), ...)

Arguments

`gr`	genomic regions, it can be a data frame or a `GRanges` object
`h1`	top/bottom positions for rectangles
`h2`	top/bottom positions for rectangles
`gp`	graphic settings, should be specified by `gpar`.
`...`	other arguments passed to `add_track`

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

require(circlize)
bed = generateRandomBed(200)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_rect_track(bed, h1 = bed[[4]], h2 = 0, 
    gp = gpar(col = NA, fill = col_fun(bed[[4]])))
require(circlize)
bed = generateRandomBed(200)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_rect_track(bed, h1 = bed[[4]], h2 = 0, 
    gp = gpar(col = NA, fill = col_fun(bed[[4]])))

add segments to a new or exsited track

Description

add segments to a new or exsited track

Usage

add_segments_track(gr, value, gp = gpar(), ...)
add_segments_track(gr, value, gp = gpar(), ...)

Arguments

`gr`	genomic regions, it can be a data frame or a `GRanges` object
`value`	numeric values associated with `gr`
`gp`	graphic settings, should be specified by `gpar`.
`...`	other arguments passed to `add_track`

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

require(circlize)
bed = generateRandomBed(nr = 100)
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_segments_track(bed, bed[[4]], gp = gpar(col = ifelse(bed[[4]] > 0, "red", "green"), lwd = 4))
require(circlize)
bed = generateRandomBed(nr = 100)
gtrellis_layout(track_ylim = range(bed[[4]]), nrow = 3, byrow = FALSE)
add_segments_track(bed, bed[[4]], gp = gpar(col = ifelse(bed[[4]] > 0, "red", "green"), lwd = 4))

Add self-defined graphics track by track

Description

Add self-defined graphics track by track

Usage

add_track(gr = NULL, category = NULL, track = current_track() + 1,
    clip = TRUE, panel_fun = function(gr) NULL, panel.fun = NULL,
    use_raster = FALSE,
    raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
    raster_quality = 1,
    raster_device_param = list())
add_track(gr = NULL, category = NULL, track = current_track() + 1,
    clip = TRUE, panel_fun = function(gr) NULL, panel.fun = NULL,
    use_raster = FALSE,
    raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
    raster_quality = 1,
    raster_device_param = list())

Arguments

`gr`	genomic regions. It should be a data frame in BED format or a `GRanges` object.
`category`	subset of categories (e.g. chromosomes) that users want to add graphics. The value can be a vector which contains more than one category. By default it is all available categories.
`track`	which track the graphics will be added to. By default it is the next track. The value should only be a scalar.
`clip`	whether graphics are restricted inside the cell.
`panel_fun`	self-defined panel function to add graphics in each 'cell'. THe argument `gr` in `panel_fun` only contains data for the current category which is a subset of the main `gr`. The function can also contains no argument if nothing needs to be passed in.
`panel.fun`	deprecated
`use_raster`	whether render the each panel as a raster image. It helps to reduce file size when the file size is huge.
`raster_device`	graphic device which is used to generate the raster image
`raster_quality`	a value set to larger than 1 will improve the quality of the raster image. A temporary image with `raster_quality`*`raster_quality` times the original size of panel is generated first and then fit into the panel by `grid.raster`.
`raster_device_param`	a list of further parameters for the selected graphic device

Details

Initialization of the Trellis layout and adding graphics are two independent steps. Once the layout initialization finished, each cell will be an independent plotting region. As same as panel_fun in circlize-package, the self-defined function panel_fun will be applied on every cell in the specified track (by default it is the 'current' track).

When adding graphics in each cell, get_cell_meta_data can return several meta data for the current cell.

Since this package is implemented by the grid graphic system, grid-family functions (such as grid.points, grid.rect, ...) should be used to add graphics. The usage of grid functions is quite similar as the traditional graphic functions. Followings are several examples:

    grid.points(x, y)
    grid.lines(x, y)
    grid.rect(x, y, width, height)

Graphical parameters are usually passed by gpar:

    grid.points(x, y, gp = gpar(col = "red")
    grid.rect(x, y, width, height, gp = gpar(fill = "black", col = "red"))

grid system also support a large number of coordinate measurement systems by defining proper unit object which provides high flexibility to place graphics on the plotting regions.

    grid.points(x, y, default.units = "npc")
    grid.rect(x, y, width = unit(1, "cm"))

You can refer to the documentations and vignettes of grid-package to get a overview.

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

The index of current track

Description

The index of current track

Usage

current_track()
current_track()

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

Get meta data in a cell

Description

Get meta data in a cell

Usage

get_cell_meta_data(name, category, track)
get_cell_meta_data(name, category, track)

Arguments

`name`	name of the supported meta data, see 'details' section.
`category`	which category. By default it is the current category.
`track`	which track. By default it is the current track.

Details

Following meta data can be retrieved:

name: name of the category.
xlim: xlim without including padding. Cells in the same column share the same xlim.
ylim: ylim without including padding.
extended_xlim: xlim with padding.
extended_ylim: ylim with padding.
original_xlim: xlim in original data.
original_ylim: ylim in original data.
column: which column in the layout.
row: which row in the layout.
track: which track in the layout.

The vignette has a graphical explanation of all these meta data.

Value

Corresponding meta data that user queried.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

Initialize genome-level Trellis layout

Description

Initialize genome-level Trellis layout

Usage

gtrellis_layout(data = NULL, category = NULL,
    species = NULL, nrow = NULL, ncol = NULL,
    n_track = 1, track_height = 1, track_ylim = c(0, 1),
    track_axis = TRUE, track_ylab = "", ylab_rot = 90, title = NULL,
    xlab = "Genomic positions", xaxis = TRUE, xaxis_bin = NULL,
    equal_width = FALSE, compact = FALSE, border = TRUE, asist_ticks = TRUE,
    xpadding = c(0, 0), ypadding = c(0, 0), gap = unit(1, "mm"),
    byrow = TRUE, newpage = TRUE, add_name_track = FALSE,
    name_fontsize = 10, name_track_fill = "#EEEEEE",
    add_ideogram_track = FALSE, ideogram_track_height = unit(2, "mm"),
    axis_label_fontsize = 6, lab_fontsize = 10, title_fontsize = 16,
    legend = list(), legend_side = c("right", "bottom"),
    padding = unit(c(2, 2, 2, 2), "mm"), remove_chr_prefix = FALSE)
gtrellis_layout(data = NULL, category = NULL,
    species = NULL, nrow = NULL, ncol = NULL,
    n_track = 1, track_height = 1, track_ylim = c(0, 1),
    track_axis = TRUE, track_ylab = "", ylab_rot = 90, title = NULL,
    xlab = "Genomic positions", xaxis = TRUE, xaxis_bin = NULL,
    equal_width = FALSE, compact = FALSE, border = TRUE, asist_ticks = TRUE,
    xpadding = c(0, 0), ypadding = c(0, 0), gap = unit(1, "mm"),
    byrow = TRUE, newpage = TRUE, add_name_track = FALSE,
    name_fontsize = 10, name_track_fill = "#EEEEEE",
    add_ideogram_track = FALSE, ideogram_track_height = unit(2, "mm"),
    axis_label_fontsize = 6, lab_fontsize = 10, title_fontsize = 16,
    legend = list(), legend_side = c("right", "bottom"),
    padding = unit(c(2, 2, 2, 2), "mm"), remove_chr_prefix = FALSE)

Arguments

`data`	a data frame with at least three columns. The first three columns should be genomic categories (e.g. chromosomes), start positions and end positions. This data frame is used to extract ranges for each genomic category (minimal and maximal positions are taken as the range in the corresponding category).
`category`	subset of categories. It is also used for ordering.
`species`	Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download `chromInfo.txt.gz` from UCSC ftp automatically. Short scaffolds will be removed if they have obvious different length as others. Non-normal chromosomes will also be detected and removed. Sometimes this detection is not always correct and if you find chromosomes shown on the plot is not what you expect, set `category` manually. The argument is passed to `read.chromInfo`.
`nrow`	Number of rows in the layout.
`ncol`	Number of columns in the layout.
`n_track`	Number of tracks in each genomic category.
`track_height`	height of tracks. It should be numeric which means the value is relative and will be scaled into percent, or a `unit` object.
`track_ylim`	ranges on y axes of tracks. The value can be a vector of length two which means all tracks share same y ranges, or a matrix with two columns, or a vector of length `2*n_track` which will be coerced into the two-column matrix by rows.
`track_axis`	whether show y axes for tracks. The value is logical that can be either length one or number of tracks.
`track_ylab`	labels for tracks on y axes. The value can be either length one or number of tracks.
`ylab_rot`	value can only be 0 or 90.
`title`	title of the plot.
`xlab`	labels on x axes.
`xaxis`	whether show x axes.
`xaxis_bin`	bin size for x axes.
`equal_width`	whether all columns in the layout have the same width. If `TRUE`, short categories will be extended according to the longest category.
`compact`	For the catgories which are put in a same row, will they be put compactly without being aligned by columns.
`border`	whether show borders.
`asist_ticks`	if axes ticks are added on one side in rows or columns, whether add ticks on the other sides.
`xpadding`	padding on x axes in each cell. Numeric value means relative ratio corresponding to the cell width. Use `I` to set it as absolute value which is measured in the data viewport (the coordinate system corresponding to the real data). Currently you cannot set it as a `unit` object.
`ypadding`	padding on y axes in each cell. Only numeric value is allowed currently.
`gap`	0 or a `unit` object. If it is length two, the first element corresponds to the gaps between rows and the second corresponds to the gaps between columns.
`byrow`	arrange categories (e.g. chromosomes) by rows or by columns in the layout.
`newpage`	whether call `grid.newpage` to create a new page.
`add_name_track`	whether add a pre-defined name track (insert before the first track). The name track is simply a track which only contains text. The default style of the name track is simple, but users can self define their own by `add_track`.
`name_fontsize`	font size for text in the name track. Note the font size also affects the height of name track.
`name_track_fill`	filled color for name track.
`add_ideogram_track`	whether to add a pre-defined ideogram track (insert after the last track). If the cytoband data for specified species is not available, this argument is ignored. The ideogram track simply contains rectangles with different colors, implemented by `add_track`.
`ideogram_track_height`	Height of ideogram track. The value should be a `unit` object.
`axis_label_fontsize`	font size for axis labels.
`lab_fontsize`	font size for x-labels and y-labels.
`title_fontsize`	font size for title.
`legend`	a `grob` or `Legends-class` object, or a list of them.
`legend_side`	side of the legend
`padding`	padding of the plot. Elements correspond to bottom, left, top, right paddings.
`remove_chr_prefix`	if chromosome names start with 'chr', whether to remove it.

Details

Genome-level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. The gtrellis_layout function arranges genomic categories on the plot in a quite flexible way. Then users apply add_track to add self-defined graphics to the plot track by track.

For more detailed demonstration of the function, please refer to the vignette.

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

Show index on each cell

Description

Show index on each cell

Usage

gtrellis_show_index()
gtrellis_show_index()

Details

The function adds name and index of track for each cell. It is only for demonstration purpose.

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

# There is no example
NULL
# There is no example
NULL

Package 'gtrellis'

Help Index

add heatmap to a new track

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Add ideogram track

Description

Usage

Arguments

Details

Value

Author(s)

Examples

add lines to a new or exsited track

Description

Usage

Arguments

Value

Author(s)

Examples

add points to a new or exsited track

Description

Usage

Arguments

Value

Author(s)

Examples

add retangles to a new or exsited track

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

add segments to a new or exsited track

Description

Usage

Arguments

Value

Author(s)

Examples

Add self-defined graphics track by track

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

The index of current track

Description

Usage

Value

Author(s)

Examples

Get meta data in a cell

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Initialize genome-level Trellis layout

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Show index on each cell