Package 'plotgardener'

Title: Coordinate-Based Genomic Visualization Package for R
Description: Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Authors: Nicole Kramer [aut, cre], Eric S. Davis [aut], Craig Wenger [aut], Sarah Parker [ctb], Erika Deoudes [art], Michael Love [ctb], Douglas H. Phanstiel [aut, cre, cph]
Maintainer: Nicole Kramer <[email protected]>, Douglas Phanstiel <[email protected]>
License: MIT + file LICENSE
Version: 1.11.3
Built: 2024-06-29 02:43:50 UTC
Source: https://github.com/bioc/plotgardener

Help Index

Check for .(m)cool file and contents

Description

Check for .(m)cool file and contents

Usage

.checkCool(file)

Arguments

file

Path to .(m)cool file

Author(s)

Sarah Parker

Error checking function for .(m)cool files

Description

Error checking function for .(m)cool files

Usage

.checkCoolErrors(
  file,
  chrom,
  chromstart,
  chromend,
  zrange,
  altchrom,
  altchromstart,
  altchromend,
  norm,
  resolution
)

Arguments

file

Path to .(m)cool file
chrom

User-inputted chromosome
chromstart

User-inputted chromstart, can still be NULL at this point.
chromend

User-inputted chromend, can still be NULL at this point.
zrange

User-inputted zrange.
altchrom

User-inputted alt chromosome.
altchromstart

User-inputted alt chromstart.
altchromend

User-inputted alt chromend.
norm

User-inputted normalization.
resolution

Resolution, either user-inputted or determined by 'auto'.

Determine best resolution for size of region for .(m)cool files

Description

Determine best resolution for size of region for .(m)cool files

Usage

.coolAutoResolution(file, chromstart, chromend)

Arguments

file

Path to .(m)cool file
chromstart

Chromstart of region
chromend

Chromend of region

Add (alt)chromstart and (alt)chromend for NULL (alt)chrom region of .(m)cool files

Description

Add (alt)chromstart and (alt)chromend for NULL (alt)chrom region of .(m)cool files

Usage

.coolRegion(file, chrom, resolution)

Arguments

file

Path to .(m)cool file
chrom

Chromosome of region; can also be altchromosome
resolution

Resolution to read chromsome info from

Read in data for a bin chunk

Description

Read in data for a bin chunk

Usage

.pullBinChunks(
  binChunk,
  file,
  bin_offsets,
  binChunkSize,
  datasetPath,
  end1bin,
  start2bin,
  end2bin
)

Arguments

binChunk

The binChunk indeces to read
file

Path to .(m)cool file
bin_offsets

Read in bin1 offsets
binChunkSize

Size of bin chunk, for comparison against the end of the bin chunk
datasetPath

Dataset path, for specifying resolution in .mcool file
end1bin

Bin where end1 starts
start2bin

Bin for chr2 starts
end2bin

Bin for end2 starts

Annotate domains in a Hi-C plot

Description

Annotate domains in a Hi-C plot

Usage

annoDomains(
    plot,
    data,
    half = "inherit",
    linecolor = "black",
    params = NULL,
    ...
)

Arguments

plot

Hi-C plot object from plotHicSquare or plotHicTriangle on which to annotate pixels.
data

A string specifying the BED file path, a dataframe in BED format, or a GRanges object specifying domain ranges.
half

Character value specifying which half of hic plots to annotate. Triangle Hi-C plots will always default to the entirety of the triangular plot. Default value is half = "inherit". Options are:

  • "inherit": Domains will be annotated on the half inherited by the input Hi-C plot.

  • "both": Domains will be annotated on both halves of the diagonal of a square Hi-C plot.

  • "top": Domains will be annotated on the upper diagonal half of a square Hi-C plot.

  • "bottom": Domains will be annotated ont the bottom diagonal half of a square Hi-C plot.

linecolor

A character value specifying the color of the domain annotations. Default value is linecolor = "black".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a domain object containing relevant genomic region, placement, and grob information.

Examples

## Define a GRanges object with TAD ranges
library(GenomicRanges)
library(IRanges)
domains <- GRanges("chr21",
    ranges = IRanges(
        start = c(28210000, 29085000, 29430000, 29700000),
        end = c(29085000, 29430000, 29700000, 30125000)
    )
)

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 4.5, height = 4, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate domains on bottom half 0f Hi-C plot
annoDomains(
    plot = hicPlot, data = domains,
    half = "bottom", linecolor = "red"
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.6, y = 0.5, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.53, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Annotate genomic coordinates along the x or y-axis of a plot

Description

Annotate genomic coordinates along the x or y-axis of a plot

Usage

annoGenomeLabel(
    plot,
    fontsize = 10,
    fontcolor = "black",
    linecolor = "black",
    margin = unit(1, "mm"),
    scale = "bp",
    commas = TRUE,
    sequence = TRUE,
    boxWidth = 0.5,
    axis = "x",
    at = NULL,
    tcl = 0.5,
    x,
    y,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

plot

Input plot to annotate genomic coordinates. Genomic coordinates and assembly will be inherited from plot.
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 10.
fontcolor

A character value indicating the color for text. Default value is fontcolor = "black".
linecolor

A character value indicating the color of the genome label axis. Default value is linecolor = "black".
margin

A numeric or unit vector specifying space between axis and coordinate labels. Default value is margin = unit(1, "mm").
scale

A character value indicating the scale of the coordinates along the genome label. Default value is scale = "bp". Options are:

  • "bp": base pairs.

  • "Kb": kilobase pairs. 1 kilobase pair is equal to 1000 base pairs.

  • "Mb": megabase pairs. 1 megabase pair is equal to 1000000 base pairs.

commas

A logical value indicating whether to include commas in start and stop labels. Default value is commas = TRUE.
sequence

A logical value indicating whether to include sequence information above the label of an x-axis (only at appropriate resolutions).
boxWidth

A numeric value indicating the width of the boxes representing sequence information at appropriate resolutions. Default value is boxWidth = 0.5.
axis

A character value indicating along which axis to add genome label. Sequence information will not be displayed along a y-axis. Default value is axis = "x". Options are:

  • "x": Genome label will be plotted along the x-axis.

  • "y": Genome label will be plotted along the y-axis. This is typically used for a square Hi-C plot made with plotHicSquare.

at

A numeric vector of x-value locations for tick marks.
tcl

A numeric specifying the length of tickmarks as a fraction of text height. Default value is tcl = 0.5.
x

A numeric or unit object specifying genome label x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying genome label y-location. The character value will place the genome label y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
just

Justification of genome label relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x or y are only given as numerics. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters or digit specifications. See gpar and formatC.

Value

Returns a genomeLabel object containing relevant genomic region, placement, and grob information.

Examples

## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Create page
pageCreate(width = 5, height = 2, default.units = "inches")

## Plot and place gene track on page
genesPlot <- plotGenes(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19", fill = c("grey", "grey"),
    fontcolor = c("grey", "grey"),
    x = 0.5, y = 0.25, width = 4, height = 1,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate x-axis genome labels at different scales
annoGenomeLabel(
    plot = genesPlot, scale = "Mb",
    x = 0.5, y = 1.25, just = c("left", "top"),
    default.units = "inches"
)
annoGenomeLabel(
    plot = genesPlot, scale = "Kb",
    x = 0.5, y = 1.5, just = c("left", "top"),
    default.units = "inches"
)
annoGenomeLabel(
    plot = genesPlot, scale = "bp",
    x = 0.5, y = 1.75, just = c("left", "top"),
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

Add a color scale legend for heatmap-style plots

Description

Add a color scale legend for heatmap-style plots

Usage

annoHeatmapLegend(
    plot,
    orientation = "v",
    fontsize = 8,
    fontcolor = "dark grey",
    scientific = FALSE,
    digits = 1,
    ticks = FALSE,
    breaks = NULL,
    border = FALSE,
    x,
    y,
    width,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

plot

Heatmap-style plot object to add heatmap legend for.
orientation

A string specifying legend orientation. Default value is orientation = "v". Options are:

  • "v": Vertical legend orientation.

  • "h": Horizontal legend orientation.

fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 8.
fontcolor

Character value specfying text fontcolor. Default value is fontcolor = "dark grey".
scientific

Logical value specifying if numeric color value labels should be encoded in scientific format. Default value is scientific = FALSE.
digits

Numeric specifying how many significant digits to include of numeric color value labels. Default value is digits = 1.
ticks

Logical value specifying if tick marks on the heatmap colorbar should be visible. Default value is ticks = FALSE.
breaks

A numeric vector specifying tick breaks. Default value is breaks = NULL.
border

Logical value indicating whether to add a border around heatmap legend. Default value is border = FALSE.
x

A numeric or unit object specifying x-location of legend.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying y-location of legend. The character value will place the legend y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying width of legend.
height

A numeric or unit object specifying height of legend.
just

Justification of heatmap legend relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a heatmapLegend object with relevant color value, placement, and grob information.

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 4, height = 3.5, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 2.5, height = 2.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Add heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.2, y = 0.5, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.03, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Annotates a highlight box around a specified genomic region of a plot

Description

Annotates a highlight box around a specified genomic region of a plot

Usage

annoHighlight(
    plot,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    fill = "grey",
    linecolor = NA,
    alpha = 0.4,
    y,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

plot

Input plot on which to annotate genomic region.
chrom

Chromosome of region to be highlighted, as a string.
chromstart

Integer start position on chromosome to be highlighted.
chromend

Integer end position on chromosome to be highlighted.
fill

A character value specifying highlight box fill color. Default value is fill = "grey".
linecolor

A character value specifying highlight box line color. Default value is linecolor = NA.
alpha

Numeric value specifying color transparency. Default value is alpha = 0.4.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying square highlight box y-location. The character value will place the highlight box y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
height

A numeric or unit object specifying highlight box height.
just

Justification of highlight box relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if y or height are only given as numerics or numeric vectors. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a highlight object containing relevant genomic region, placement, and grob information.

Examples

## Create a page
pageCreate(width = 7.5, height = 1.5, default.units = "inches")

## Plot and place a signal plot
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    range = c(0, 45)
)
signalPlot <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = region,
    x = 0.5, y = 0.25, width = 6.5, height = 0.65,
    just = c("left", "top"),
    default.units = "inches"
)

## Highlight genomic region on signal plot
annoHighlight(
    plot = signalPlot,
    chrom = "chr21",
    chromstart = 29000000, chromend = 29125000,
    y = 0.25, height = 1, just = c("left", "top"),
    default.units = "inches"
)

## Plot text label
plotText(
    label = "region of interest", fontsize = 8, fontcolor = "black",
    x = 3.5, y = 0.2, just = "bottom", default.units = "inches"
)

## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.3, length = 6.5, default.units = "inches"
)

## Hide page guides
pageGuideHide()

Annotate pixels in a Hi-C plot

Description

Annotate pixels in a Hi-C plot

Usage

annoPixels(
    plot,
    data,
    type = "box",
    half = "inherit",
    shift = 4,
    params = NULL,
    quiet = FALSE,
    ...
)

Arguments

plot

Hi-C plot object from plotHicSquare or plotHicTriangle on which to annotate pixels.
data

A string specifying the BEDPE file path, a dataframe in BEDPE format specifying pixel positions, or a GInteractions object specifying pixel positions.
type

Character value specifying type of annotation. Default value is type = "box". Options are:

  • "box": Boxes are drawn around each pixel.

  • "circle": Circles are drawn around each pixel.

  • "arrow": Arrows are drawn pointing to each pixel.

half

Character value specifying which half of hic plots to annotate. Triangle Hi-C plots will always default to the entirety of the triangular plot. Default value is half = "inherit". Options are:

  • "inherit": Pixels will be annotated on the half inherited by the input Hi-C plot.

  • "both": Pixels will be annotated on both halves of the diagonal of a square Hi-C plot.

  • "top": Pixels will be annotated on the upper diagonal half of a square Hi-C plot.

  • "bottom": Pixels will be annotated on the bottom diagonal half of a square Hi-C plot.

shift

Numeric specifying the number of pixels on either end of main pixel in a box or circle. Numeric specifying number of pixels for the length of an arrow.
params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.
...

Additional grid graphical parameters. See gpar.

Value

Returns a pixel object containing relevant genomic region, placement, and grob information.

Examples

## Load Hi-C data and BEDPE data
library(plotgardenerData)
data("IMR90_HiC_10kb")
data("IMR90_DNAloops_pairs")

## Create page
pageCreate(width = 4.5, height = 4, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate loops of both sides of Hi-C plot with squares
pixels <- annoPixels(
    plot = hicPlot, data = IMR90_DNAloops_pairs, type = "box",
    half = "both"
)

## Annotate loops on one side of Hi-C plot with arrows
## and the other side with circles
pagePlotRemove(plot = pixels)
pixels1 <- annoPixels(
    plot = hicPlot, data = IMR90_DNAloops_pairs,
    type = "arrow", half = "top", shift = 8
)
pixels2 <- annoPixels(
    plot = hicPlot, data = IMR90_DNAloops_pairs,
    type = "circle", half = "bottom"
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.6, y = 0.5, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.53, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Annotates a line segment within a plot

Description

Annotates a line segment within a plot

Usage

annoSegments(
    x0,
    y0,
    x1,
    y1,
    plot,
    default.units = "native",
    linecolor = "black",
    lwd = 1,
    lty = 1,
    lineend = "butt",
    linejoin = "mitre",
    arrow = NULL,
    params = NULL,
    ...
)

Arguments

x0

A numeric vector or unit object indicating the starting x-values of the line segments.
y0

A numeric vector or unit object indicating the starting y-values of the line segments.
x1

A numeric vector or unit object indicating the stopping x-values of the line segments.
y1

A numeric vector or unit object indicating the stopping y-values of the line segments.
plot

Input plotgardener plot to internally plot line segments relative to.
default.units

A string indicating the default units to use if x0, y0, x1, or y1 are only given as numeric vectors. Default value is default.units = "native".
linecolor

A character value specifying segment line color. Default value is linecolor = "black".
lwd

A numeric specifying segment line width. Default value is lwd = 1.
lty

A numeric specifying segment line type. Default value is lty = 1.
lineend

A character value specifying line end style. Default value is lineend = "butt". Options are:

  • "round": Segment ends are rounded.

  • "butt": Segment ends end exactly where ended.

  • "square": Segment ends are squared.

linejoin

A character value specifying line join style. Default value is linejoin = "mitre". Options are:

  • "round": Line joins are rounded.

  • "mitre": Line joins are sharp corners.

  • "bevel": Line joins are flattened corners.

arrow

A list describing arrow heads to place at either end of the line segments, as produced by the arrow function.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a segments object containing relevant placement and grob information.

See Also

grid.segments, arrow

Examples

library(grid)
## Create a page
pageCreate(width = 7.5, height = 2.5, default.units = "inches")

## Plot a Manhattan plot
library(plotgardenerData)
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
data("hg19_insulin_GWAS")
manhattanPlot <- plotManhattan(
    data = hg19_insulin_GWAS, assembly = "hg19",
    fill = c("grey", "#37a7db"),
    sigLine = TRUE,
    col = "grey", lty = 2, range = c(0, 14),
    x = 0.5, y = 0, width = 6.5, height = 2,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = manhattanPlot, x = 0.5, y = 2, fontsize = 8,
    just = c("left", "top"),
    default.units = "inches"
)
plotText(
    label = "Chromosome", fontsize = 8,
    x = 3.75, y = 2.20, just = "center", default.units = "inches"
)

## Annotate y-axis
annoYaxis(
    plot = manhattanPlot, at = c(0, 2, 4, 6, 8, 10, 12, 14),
    axisLine = TRUE, fontsize = 8
)

## Annotate a line segment for an additional significance line of
## the Manhattan plot
annoSegments(
    x0 = unit(0, "npc"), y0 = 10,
    x1 = unit(1, "npc"), y1 = 10,
    plot = manhattanPlot, default.units = "native",
    linecolor = "red", lty = 2
)

## Plot y-axis label
plotText(
    label = "-log10(p-value)", x = 0.15, y = 1, rot = 90,
    fontsize = 8, fontface = "bold", just = "center",
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

Annotates text within a plot

Description

Annotates text within a plot

Usage

annoText(
    label,
    fontcolor = "black",
    fontsize = 12,
    rot = 0,
    check.overlap = FALSE,
    plot,
    x,
    y,
    just = "center",
    default.units = "native",
    params = NULL,
    ...
)

Arguments

label

Character or expression of text to be plotted.
fontcolor

A character value specifying text fontcolor. Default value is fontcolor = "black".
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 12.
rot

A numeric specifying the angle to rotate the text. Default value is rot = 0.
check.overlap

A logical value to indicate whether to check for and omit overlapping text. Default value is check.overlap = FALSE.
plot

Input plotgardener plot to internally place text relative to.
x

A numeric vector or unit object specifying text x-location.
y

A numeric vector or unit object specifying text y-location.
just

Justification of text relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = "center".
default.units

A string indicating the default units to use if x or y are only given as numerics or numeric vectors. Default value is default.units = "native".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a text object containing relevant placement and grob information.

See Also

grid.text

Examples

## Create a page
pageCreate(width = 4, height = 4, default.units = "inches")

## Plot text relative to a plotgardener plot
library(plotgardenerData)
data("IMR90_HiC_10kb")
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, chrom = "chr21",
    chromstart = 28000000, chromend = 29500000,
    assembly = "hg19",
    zrange = c(0, 70),
    x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches"
)
annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.55, scale = "Mb",
    just = c("left", "top"), default.units = "inches"
)

annoText(
    label = "Loop", fontsize = 8, plot = hicPlot,
    x = 29075000, y = 28150000,
    just = "center", default.units = "native"
)

## Hide page guides
pageGuideHide()

Add an x-axis to a plot

Description

Add an x-axis to a plot

Usage

annoXaxis(
    plot,
    at = NULL,
    label = TRUE,
    main = TRUE,
    scipen = 999,
    axisLine = FALSE,
    params = NULL,
    ...
)

Arguments

plot

Plot object to annotate with x-axis.
at

A numeric vector of x-value locations for tick marks.
label

A logical value indicating whether to draw the labels on the tick marks, or an expression or character vector which specify the labels to use. If not logical, must be the same length as the at argument.
main

A logical value indicating whether to draw the x-axis at the bottom of the plot. Default value is main = TRUE. Options are:

  • TRUE: x-axis is drawn at the bottom of the plot.

  • FALSE: x-axis is drawn at the top of the plot.

scipen

An integer indicating the penalty to be applied when deciding to print numeric values in fixed or exponential notation. Default value is scipen = 999.
axisLine

A logical value indicating whether to show the axis line. Default value is axisLine = FALSE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a xaxis object containing relevant grob information.

Examples

## Load transcript information
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Create page
pageCreate(width = 7.5, height = 4.5, default.units = "inches")

## Plot gene transcripts
transcriptPlot <- plotTranscripts(
    chrom = "chr1",
    chromstart = 1000000,
    chromend = 2000000,
    assembly = "hg19",
    x = 0.5, y = 0,
    width = 6.5, height = 4,
    just = c("left", "top"),
    default.units = "inches"
)

## Add standard x-axis to transcript plot
annoXaxis(
    plot = transcriptPlot,
    at = c(1000000, 1250000, 1500000, 1750000, 2000000),
    fontsize = 8
)
plotText(
    label = "Basepairs", fontsize = 10, fontface = "bold",
    x = 3.75, y = 4.3, just = "top"
)

## Hide page guides
pageGuideHide()

Add a y-axis to a plot

Description

Add a y-axis to a plot

Usage

annoYaxis(
    plot,
    at = NULL,
    label = TRUE,
    main = TRUE,
    scipen = 999,
    axisLine = FALSE,
    params = NULL,
    ...
)

Arguments

plot

Plot object to annotate with y-axis.
at

A numeric vector of y-value locations for tick marks.
label

A logical value indicating whether to draw the labels on the tick marks, or an expression or character vector which specify the labels to use. If not logical, must be the same length as the at argument.
main

A logical value indicating whether to draw the y-axis at the left of the plot. Default value is main = TRUE. Options are:

  • TRUE: y-axis is drawn at the left of the plot.

  • FALSE: y-axis is drawn at the right of the plot.

scipen

An integer indicating the penalty to be applied when deciding to print numeric values in fixed or exponential notation. Default value is scipen = 999.
axisLine

A logical value indicating whether to show the axis line. Default value is axisLine = FALSE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a yaxis object containing relevant grob information.

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 4, height = 3.5, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 1, y = 0.5, width = 2.5, height = 2.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Add standard y-axis to Hi-C plot
annoYaxis(
    plot = hicPlot, at = c(28000000, 29000000, 30300000),
    fontsize = 10
)

## Annotate genome label on x-axis
annoGenomeLabel(plot = hicPlot, x = 1, y = 3.03)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.6, y = 0.5, width = 0.12, height = 1.2
)

## Hide page guides
pageGuideHide()

Annotates zoom lines for a specified genomic region of a plot

Description

Annotates zoom lines for a specified genomic region of a plot

Usage

annoZoomLines(
    plot,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    y0,
    x1 = NULL,
    y1,
    extend = 0,
    default.units = "inches",
    linecolor = "grey",
    lty = 2,
    params = NULL,
    ...
)

Arguments

plot

Input plot to annotate genomic region zoom lines from.
chrom

Chromosome of region to draw zoom lines from, as a string.
chromstart

Integer start position on chromosome to draw zoom lines from.
chromend

Integer end position on chromosome to draw zoom lines from.
y0

A numeric vector or unit object indicating the starting y-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line.
x1

A numeric vector or unit object indicating the stopping x-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line. If NULL, straight lines from zoomed genomic region will be drawn.
y1

A numeric vector or unit object indicating the stopping y-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line.
extend

A numeric vector or unit object indicating the length to extend straight lines from each end of the zoom line segments. If two values are given, the first value will correspond to the top extension length and the second value will correspond to the bottom extension length. Default value is extend = 0.
default.units

A string indicating the default units to use if y0, x1, y1, or extend are only given as numerics or numeric vectors. Default value is default.units = "inches".
linecolor

A character value specifying zoom line color. Default value is linecolor = "grey".
lty

A numeric specifying zoom line type. Default value is lty = 2.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a zoom object containing relevant genomic region, placement, and grob information.

Examples

## Create a page
pageCreate(width = 7.5, height = 4.75, default.units = "inches")

## Plot and place a Manhattan plot
library(plotgardenerData)
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
data("hg19_insulin_GWAS")
manhattanPlot <- plotManhattan(
    data = hg19_insulin_GWAS, assembly = "hg19",
    fill = c("grey", "#37a7db"),
    sigLine = FALSE,
    col = "grey", lty = 2, range = c(0, 14),
    x = 0.5, y = 0, width = 6.5, height = 2,
    just = c("left", "top"),
    default.units = "inches"
)
annoYaxis(
    plot = manhattanPlot, at = c(0, 2, 4, 6, 8, 10, 12, 14),
    axisLine = TRUE, fontsize = 8
)

## Annotate zoom lines for a region on chromsome 21
zoomRegion <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19"
)
annoZoomLines(
    plot = manhattanPlot, params = zoomRegion,
    y0 = 2, x1 = c(0.5, 7), y1 = 2.5, extend = c(0, 1.1),
    default.units = "inches",
    lty = 3
)

## Annotate highlight region for zoom region
annoHighlight(
    plot = manhattanPlot, params = zoomRegion,
    y = 2, height = 2, just = c("left", "bottom"),
    default.units = "inches",
    fill = "red", alpha = 0.8
)

## Plot Manhattan plot data and signal track under zoom lines
manhattanPlotZoom <- plotManhattan(
    data = hg19_insulin_GWAS,
    fill = "grey",
    sigLine = FALSE,
    baseline = TRUE,
    params = zoomRegion, range = c(0, 14),
    x = 0.5, y = 2.6,
    width = 6.5, height = 1
)
data("IMR90_ChIP_H3K27ac_signal")
signalPlot <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = zoomRegion,
    range = c(0, 45),
    x = 0.5, y = "b0.1",
    width = 6.5, height = 0.65,
    just = c("left", "top"),
    default.units = "inches"
)

## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 4.4, length = 6.5,
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

Make a assembly object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages

Description

Make a assembly object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages

Usage

assembly(
    Genome,
    TxDb,
    OrgDb,
    gene.id.column = "ENTREZID",
    display.column = "SYMBOL",
    BSgenome = NULL
)

Arguments

Genome

String indicating the name of the genome assembly.
TxDb

String of existing TxDb package name or a TxDb object.
OrgDb

String of the desired OrgDb package name.
gene.id.column

String of the TxDb column name that refers to the given TxDb gene IDs. Default value is gene.id.column = "ENTREZID".
display.column

String of the OrgDb column name that refers to the type of gene symbol to be displayed in plots. Default value is display.column = "SYMBOL".
BSgenome

String of the desired BSgenome package name.

Value

Returns a assembly object containing all input parameters.

See Also

TxDb, OrgDb-class, BSgenome

Examples

## Create a custom `assembly` object for hg38/GRCh38 packages
newAssembly <- assembly(
    Genome = "hg38_GRCh38",
    TxDb = "TxDb.Hsapiens.UCSC.hg38.knownGene",
    OrgDb = "org.Hs.eg.db",
    BSgenome = "BSgenome.Hsapiens.NCBI.GRCh38"
)

Combine multiple pgParams objects into a vector

Description

Combine multiple pgParams objects into a vector

Usage

c(..., recursive = FALSE)

Arguments

...

pgParams objects to be concatenated.
recursive

logical. If recursive = TRUE, the function recursively descends through lists (and pairlists) combining all their elements into a vector.

Value

NULL or an expression or a vector of an appropriate mode. (With no arguments the value is NULL.)

Examples

## Define parameters
p1 <- pgParams(chrom = "chr1", assembly = "hg19")

## Define another set of parameters
p2 <- pgParams(fontsize = 10, assembly = "hg19")

## Combine parameters into one `pgParams` object
pTotal <- c(p1, p2)

Calculate a score range for multiple signals

Description

Calculate a score range for multiple signals

Usage

calcSignalRange(
    data,
    chrom = NULL,
    chromstart = 1,
    chromend = .Machine$integer.max,
    assembly = "hg38",
    negData = FALSE)

Arguments

data

List of data to be plotted as character values specifying multiple bigwig file paths, dataframes in BED format, or GRanges objects with metadata column score.
chrom

Chromosome of data region ragne as a string, if range for a specific chromosome is desired.
chromstart

Integer start position on chromosome to get data range.
chromend

Integer end position on chromosome to get data range.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
negData

A logical value indicating whether any of the data has both positive and negative scores and the signal range should be adjusted accordingly. Default value is negData = FALSE.

Value

Returns a vector of length 2 with the calculated c(min, max) range.

Examples

library("plotgardenerData")
data("GM12878_ChIP_CTCF_signal")
data("IMR90_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
data("IMR90_ChIP_H3K27ac_signal")

calcSignalRange(data = list(GM12878_ChIP_CTCF_signal, 
                            GM12878_ChIP_H3K27ac_signal, 
                            IMR90_ChIP_CTCF_signal, 
                            IMR90_ChIP_H3K27ac_signal),
                chrom = "chr21",
                chromstart = 28150000, chromend = 29150000,
                assembly = "hg38", negData = FALSE)

Handle plotgardener color scaling parameters

Description

colorby should be used to create a set of parameters that specify color scaling for the functions plotPairs, plotPairsArches, and plotRanges.

Usage

colorby(column, palette = NULL, range = NULL, scalePerRegion = FALSE)

Arguments

column

String specifying name of data column to scale colors by.
palette

(optional) A function describing the color palette to use for color scaling.
range

(optional) A numeric vector specifying the range of values to apply a color scale to.
scalePerRegion

A logical value indicating whether to adjust NULL range of numerical 'colorby' values to subset of data in a plotted genomic region. Default value is scalePerRegion = FALSE.

Value

Returns a "colorby" object.

Examples

## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Add a length column
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

## Plot pairs with colorby object set for `length` column
bedpePlot <- plotPairs(
    data = IMR90_DNAloops_pairs,
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    fill = colorby("length", palette = 
                colorRampPalette(c("dodgerblue2", "firebrick2"))),
    lwd = 2, spaceHeight = .7,
)

Display the default genomic annotation packages associated with a genome build

Description

Display the default genomic annotation packages associated with a genome build

Usage

defaultPackages(Genome)

Arguments

Genome

String indicating the name of the genome assembly.

Value

Returns a list of the default data packages for a genome build.

Examples

## View default genomic annotation packages associated with "hg19"
defaultPackages(Genome = "hg19")

## View default genomic annotation packages associated with "mm9"
defaultPackages(Genome = "mm9")

Display the included available default genome assemblies

Description

Display the included available default genome assemblies

Usage

genomes()

Value

Returns the included available default genome assemblies

Examples

genomes()

Maps a numeric or character vector to a color palette and returns the vector of colors

Description

Maps a numeric or character vector to a color palette and returns the vector of colors

Usage

mapColors(vector, palette, range = NULL)

Arguments

vector

Vector to map to color.
palette

Color palette function.
range

Range of values to map for a numerical value.

Details

This function allows for the manual mapping of a numerical or factor vector to a palette of colors. For a more automatic implementation of this functionality in plotgardener functions, colorby objects can be used.

Value

Returns a character vector of color values. If the input vector is numerical, this vector will have additional 'palette' and 'range' attributes.

See Also

colorby

Examples

## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Add a length column
IMR90_DNAloops_pairs$length <- (IMR90_DNAloops_pairs$start2 - 
        IMR90_DNAloops_pairs$start1) / 1000

## Map length column to a vector of colors
colors <- mapColors(vector = IMR90_DNAloops_pairs$length,
            palette = colorRampPalette(c("dodgerblue2", "firebrick2")))
            
## Pass color vector into bbPlotPairsArches
heights <- IMR90_DNAloops_pairs$length / max(IMR90_DNAloops_pairs$length)    
pageCreate(width = 7.5, height = 2.1, default.units = "inches",
            showGuides = FALSE, xgrid = 0, ygrid = 0)       
params <- pgParams(
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    width = 7
)

archPlot <- plotPairsArches(
    data = IMR90_DNAloops_pairs, params = params,
    fill = colors,
    linecolor = "fill",
    archHeight = heights, alpha = 1,
    x = 0.25, y = 0.25, height = 1.5,
    just = c("left", "top"),
    default.units = "inches"
)            

annoGenomeLabel(plot = archPlot, x = 0.25, y = 1.78, scale = "Mb") 
annoHeatmapLegend(
    plot = archPlot, fontcolor = "black",
    x = 7.0, y = 0.25,
    width = 0.10, height = 1, fontsize = 10
)
plotText(
    label = "Kb", rot = 90, x = 6.9, y = 0.75,
    just = c("center", "center"),
    fontsize = 10
)

Create a page for a plotgardener layout

Description

Create a page for a plotgardener layout

Usage

pageCreate(
    width = 8.5,
    height = 11,
    default.units = "inches",
    bg = NA,
    xgrid = 0.5,
    ygrid = 0.5,
    showGuides = TRUE,
    params = NULL
)

Arguments

width

A numeric or unit object specifying page width. Default value is width = 8.
height

A numeric or unit object specifying page height. Default value is height = 11.
default.units

A string indicating the default units to use if width or height are only given as numerics. Default value is default.units = "inches".
bg

Character value indicating page background color. Default value is bg = NA.
xgrid

A numeric indicating the increment by which to place vertical gridlines. Default value is xgrid = 0.5.
ygrid

A numeric indicating the increment by which to place horizontal gridlines. Default value is ygrid = 0.5.
showGuides

A logical value indicating whether to draw a black border around the entire page and guiding rulers along the top and left side of the page. Default value is showOutline = TRUE.
params

An optional pgParams object containing relevant function parameters.

Details

width and height must be specified in the same units.

Value

None.

Examples

## Create a 6-inch wide, 4.5-inch high page
pageCreate(width = 6, height = 4.5, default.units = "inches")

## Create a 14-cm wide, 10-cm high page
pageCreate(width = 14, height = 10, default.units = "cm")

Remove guides from a plotgardener page

Description

Remove guides from a plotgardener page

Usage

pageGuideHide()

Value

None.

Note

Please note that due to the implementation of 'grid' removal functions, using 'pageGuideHide' within a 'pdf' call will result in the rendering of a separate, new page with the plot guides removed. To avoid this artifact, hide guides in the 'pageCreate' function call with 'showGuides = FALSE'.

Examples

## Make a page
pageCreate(width = 7, height = 4, default.units = "inches")

## Hide page guides
pageGuideHide()

Draw a horizontal guideline at a specified y-coordinate on a plotgardener page

Description

Draw a horizontal guideline at a specified y-coordinate on a plotgardener page

Usage

pageGuideHorizontal(
    y,
    default.units = "inches",
    linecolor = "grey55",
    params = NULL,
    ...
)

Arguments

y

A numeric or unit object specifying y-coordinate of guide.
default.units

A string indicating the default units to use if y is only given as a numeric. Default value is default.units = "inches".
linecolor

Character value indicating color of guideline. Default value is linecolor = "grey55".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

None.

Examples

## Create a page
pageCreate(width = 6, height = 5, default.units = "inches")

## Add red horizontal guideline at y = 2.5 inches
pageGuideHorizontal(y = 2.5, linecolor = "red")

Reshow guides drawn with pageCreate, pageGuideHorizontal, and pageGuideVertical

Description

Reshow guides drawn with pageCreate, pageGuideHorizontal, and pageGuideVertical

Usage

pageGuideShow()

Value

None.

See Also

pageCreate, pageGuideHorizontal, pageGuideVertical

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 3, height = 3, default.units = "inches")

## Add a page guide
pageGuideHorizontal(y = 0.5, default.units = "inches")

## Plot and place Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    x = 0.5, y = 0.5, width = 2, height = 2,
    just = c("left", "top"),
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

## Re-show page guides
pageGuideShow()

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "x",
    x = 0.5, y = 2.53, just = c("left", "top")
)

Draw a vertical guideline at a specified x-coordinate on a plotgardener page

Description

Draw a vertical guideline at a specified x-coordinate on a plotgardener page

Usage

pageGuideVertical(
    x,
    default.units = "inches",
    linecolor = "grey55",
    params = NULL,
    ...
)

Arguments

x

A numeric or unit object specifying x-coordinate of guide.
default.units

A string indicating the default units to use if x is only given as a numeric. Default value is default.units = "inches".
linecolor

Character value indicating color of guideline. Default value is linecolor = "grey55".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

None.

Examples

## Create a page
pageCreate(width = 6, height = 5, default.units = "inches")

## Add blue vertical guideline at x = 1.7 inches
pageGuideVertical(x = 1.7, linecolor = "blue")

Generate column positions for a number of plot elements with a specified width and space between them

Description

Generate column positions for a number of plot elements with a specified width and space between them

Usage

pageLayoutCol(x, width, space, n, default.units = "inches")

Arguments

x

A numeric or unit object specifying the starting column x-position.
width

A numeric or unit object specifying the width of columns.
space

A numeric or unit object specifying the space between columns.
n

An integer specifying the number of elements to generate column positions for.
default.units

A string indicating the default units to use if x, w, or s are only given as numerics. Default value is default.units = "inches"

Value

Returns a unit vector of page positions.

Examples

# Starting at 0.5 units, return a vector of positions for 3 objects that
# are 2 units in width with 0.1 units of space between them

pageLayoutCol(x = 0.5, width = 2, space = 0.1, n = 3, 
            default.units = "inches")

Generate row positions for a number of plot elements with a specified height and space between them

Description

Generate row positions for a number of plot elements with a specified height and space between them

Usage

pageLayoutRow(y, height, space, n, default.units = "inches")

Arguments

y

A numeric or unit object specifying the starting row y-position.
height

A numeric or unit object specifying the height of rows.
space

A numeric or unit object specifying the space between rows.
n

An integer specifying the number of elements to generate row positions for.
default.units

A string indicating the default units to use if y, h, or s are only given as numerics. Default value is default.units = "inches".

Value

Returns a unit vector of page positions.

Examples

# Starting at 0.5 units, return a vector of positions for 3 objects that
# are 2 units in height with 0.1 units of space between them

pageLayoutRow(y = 0.5, height = 2, space = 0.1, n = 3, 
            default.units = "inches")

Place a plot that has been previously created but not drawn

Description

Place a plot that has been previously created but not drawn

Usage

pagePlotPlace(
    plot,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL
)

Arguments

plot

Plot object to be placed, defined by the output of a plotgardener plotting function.
x

A numeric or unit object specifying plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying plot y-location. The character value will place the plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying plot width.
height

A numeric or unit object specifying plot height.
just

Justification of plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.

Value

Function will update dimensions of an input plot and return an updated plot object.

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create, but do not plot, square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    draw = FALSE
)

## Create page
pageCreate(width = 3.75, height = 3.5, default.units = "inches")

## Place Hi-C plot on page
pagePlotPlace(
    plot = hicPlot,
    x = 0.25, y = 0.25, width = 3, height = 3,
    just = c("left", "top"),
    default.units = "inches", draw = TRUE
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.4, y = 0.25, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Hide page guides
pageGuideHide()

Remove plotgardener plots and annotations

Description

Remove plotgardener plots and annotations

Usage

pagePlotRemove(plot)

Arguments

plot

Plot object to be removed, defined by the output of a plotgardener plotting function.

Value

None.

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 5.5, height = 4, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    x = 0.5, y = 0.5, width = 2.5, height = 2.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Remove square Hi-C plot from page
pagePlotRemove(plot = hicPlot)

pgParams: plotgardener parameters object

Description

Creates an object of class "pgParams" that can be used by plotgardener functions. pgParams can be used to set a set of parameters to be shared across multiple functions.

Usage

pgParams(assembly = "hg38", gene = NULL, geneBuffer = NULL, ...)

Arguments

assembly

String defining the genome build. Default value is assembly = "hg38".
gene

(optional) String naming a gene used to set the chrom, chromstart, and chromend arguments.
geneBuffer

(optional) Integer base-pairs to extend the start and end of a gene defined by argument gene. Can be one integer or a vector of length 2, where the first integer will extend the start of the gene and the second integer will extend the end of the gene.
...

This function will take any plotgardener function parameters and their values:

  • alpha

  • altchrom

  • altchromend

  • altchromstart

  • archHeight

  • arrow

  • at

  • axis

  • axisLine

  • baseline

  • baseline.color

  • baseline.lwd

  • bg

  • binCap

  • binSize

  • border

  • boxHeight

  • boxWidth

  • breaks

  • BSgenome

  • cex

  • check.overlap

  • chrom

  • chromend

  • chromstart

  • clip

  • collapse

  • colorbyStrand

  • colorTrans

  • column

  • commas

  • curvature

  • data

  • default.units

  • digits

  • display.column

  • draw

  • extend

  • file

  • fill

  • flip

  • fontcolor

  • fontsize

  • geneBackground

  • geneHighlights

  • gene.id.column

  • geneOrder

  • Genome

  • half

  • height

  • id

  • id.lengths

  • image

  • interpolate

  • just

  • label

  • labels

  • leadSNP

  • legend

  • length

  • limitLabel

  • linecolor

  • lineend

  • linejoin

  • lty

  • lwd

  • main

  • margin

  • matrix

  • negData

  • norm

  • OrgDb

  • orientation

  • palette

  • pch

  • plot

  • quiet

  • r

  • range

  • resolution

  • res_scale

  • rot

  • scale

  • scientific

  • scipen

  • sequence

  • shift

  • showBands

  • showGuides

  • sigCol

  • sigLine

  • sigVal

  • spaceHeight

  • spaceWidth

  • strand

  • strandLabels

  • strandSplit

  • stroke

  • style

  • tcl

  • ticks

  • title

  • TxDb

  • type

  • width

  • x

  • xgrid

  • x0

  • x1

  • y

  • ygrid

  • ymax

  • y0

  • y1

  • zrange

Details

pgParams generates arguments from exported plotgardener functions at loading time of the package. Arguments defined in a pgParams object can be passed into the params argument of plotgardener functions. params arguments can be overridden from within plotgardener functions.

pgParams also provides an alternative region definition mechanism. Given a gene name and genome assembly, pgParams returns the appropriate "chrom", "chromstart", and "chromend" with a default buffer of (gene length) / 2 added to the ends of the gene coordinates. The buffer amount can be set manually with the geneBuffer parameter. Buffer extending beyond the length of the chromosome will be trimmed.

Value

Returns an object of class pgParams containing plotgardener function arguments.

Examples

## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Define parameters
p1 <- pgParams(gene = "IL1B", assembly = "hg19")

## Optionally add more parameters
p2 <- pgParams(fontsize = 10, assembly = "hg19")

## Combine parameters and pass them to a plotgardener function
plotGenes(params = c(p1, p2))

Plot a circle within a plotgardener layout

Description

Plot a circle within a plotgardener layout

Usage

plotCircle(
    x,
    y,
    r,
    default.units = "inches",
    linecolor = "black",
    lwd = 1,
    lty = 1,
    fill = NA,
    alpha = 1,
    params = NULL,
    ...
)

Arguments

x

A numeric vector or unit object specifying circle x-locations relative to center.
y

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying circle y-locations relative to center. The character vector will place circle y-locations relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
r

A numeric vector or unit object specifying radii.
default.units

A string indicating the default units to use if r, x, or y are only given as numerics or numeric vectors. Default value is default.units = "inches".
linecolor

A character value specifying circle line color. Default value is linecolor = "black".
lwd

A numeric specifying circle line width. Default value is lwd = 1.
lty

A numeric specifying circle line type. Default value is lty = 1.
fill

A character value specifying circle fill color. Default value is fill = NA.
alpha

Numeric value specifying color transparency. Default value is alpha = 1.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a circle object containing relevant placement and grob information.

See Also

grid.circle

Examples

## Create a page
pageCreate(width = 2, height = 2, default.units = "inches")

## Plot two circles, one at a time
plotCircle(
    x = 0.6, y = 0.5, r = 0.1, fill = "black",
    default.units = "inches"
)
plotCircle(
    x = 1.4, y = 0.5, r = 0.1, fill = "black",
    default.units = "inches"
)

## Plot a vector of circles
xVals <- 1 + (0.5 * cos(seq(0, pi, pi / 8)))
yVals <- 1 + (0.5 * sin(seq(0, pi, pi / 8)))
plotCircle(x = xVals, y = yVals, r = 0.05, default.units = "inches")

## Hide page guides
pageGuideHide()

plotgardener: Coordinate-based Genomic Visualization Package for R

Description

plotgardener is a coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Author(s)

Maintainer: Nicole Kramer [email protected] (ORCID)

Authors:

Other contributors:

See Also

Useful links:

Plot a gene track for a specified genomic region

Description

Plot a gene track for a specified genomic region

Usage

plotGenes(
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fontsize = 8,
    fontcolor = c("#669fd9", "#abcc8e"),
    fill = c("#669fd9", "#abcc8e"),
    geneOrder = NULL,
    geneHighlights = NULL,
    geneBackground = "grey",
    strandLabels = TRUE,
    stroke = 0.1,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = unit(0.6, "inches"),
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL
)

Arguments

chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 8.
fontcolor

A character value or vector of length 2 indicating the fontcolors for the plus strand and minus strand gene labels. The first value will color the plus strand gene labels and the second value will color the minus strand gene labels. Default value is fontcolor = c("#669fd9", "#abcc8e").
fill

A character value or vector of length 2 indicating the strand fill colors for the plus strand and minus strand plot elements. The first value will color the plus strand plot elements and the second label will color the minus strand plot elements. Default value is fill = c("#669fd9", "#abcc8e").
geneOrder

An ordered character vector of gene names to prioritize when labeling genes.
geneHighlights

A two-column dataframe with a column named "gene" containing gene names as strings to highlight and a named column "color" containing corresponding highlight colors.
geneBackground

If geneHighlights is given, a character value indicating the color for genes that are not highlighted.
strandLabels

A logical value indicating whether to include + and - strand labels to the left of the gene track.
stroke

A numeric value indicating the stroke width for gene body outlines. Default value is stroke = 0.1.
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying genes plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying genes plot y-location. The character value will place the genes plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying genes plot width.
height

A numeric or unit object specifying genes plot height.
just

Justification of genes plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.

Details

A gene track can be placed on a page by providing plot placement parameters: 

plotGenes(chrom, chromstart = NULL, chromend = NULL,
            x, y, width, height, just = c("left", "top"),
            default.units = "inches")

This function can be used to quickly plot an unnannotated gene track by ignoring plot placement parameters: 

plotGenes(chrom, chromstart = NULL, chromend = NULL)

Genomic annotation information is acquired through TxDb and OrgDb-class packages, as determined through the assembly parameter. To avoid overcrowding of gene name labels, plotted gene labels are by default prioritized according to citation counts.

Value

Returns a genes object containing relevant genomic region, placement, and grob information.

See Also

assembly, genomes, defaultPackages

Examples

## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Set genomic coordinates
paramssmall <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 3000000,
    assembly = "hg19", width = 7
)
paramsbig <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 146364022,
    assembly = "hg19", width = 7
)
## Set colors
cols <- c("#41B6C4", "#225EA8")

## Create page
pageCreate(width = 7.5, height = 3.5, default.units = "inches")

## Plot genes big
genesPlot <- plotGenes(
    params = paramsbig, fill = cols,
    fontcolor = cols,
    x = 0.25, y = 0.25, height = 0.75,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = genesPlot, x = 0.25, y = 1.0,
    scale = "Mb", just = c("left", "top")
)

## Plot genes small
genesPlot <- plotGenes(
    params = paramssmall,
    geneHighlights = data.frame(
        "gene" = c("DLGAP2"),
        "color" = c("#225EA8")
    ),
    geneBackground = "grey",
    x = 0.25, y = 2.25, height = 0.75,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = genesPlot, x = 0.25, y = 3.0, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Plot genomic coordinates along the x or y-axis of a plotgardener plot

Description

Plot genomic coordinates along the x or y-axis of a plotgardener plot

Usage

plotGenomeLabel(
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fontsize = 10,
    fontcolor = "black",
    linecolor = "black",
    margin = unit(1, "mm"),
    scale = "bp",
    commas = TRUE,
    sequence = TRUE,
    boxWidth = 0.5,
    axis = "x",
    at = NULL,
    tcl = 0.5,
    x,
    y,
    length,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

chrom

Chromosome of genome label, as a string, or a character vector of chromosomes for a whole genome Manhattan plot.
chromstart

Integer start of genome label.
chromend

Integer end of genome label.
assembly

Default genome assembly as a string or a assembly object.
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 10.
fontcolor

A character value indicating the color for text. Default value is fontcolor = "black".
linecolor

A character value indicating the color of the genome label axis. Default value is linecolor = "black".
margin

A numeric or unit vector specifying space between axis and coordinate labels. Default value is margin = unit(1, "mm"),
scale

A character value indicating the scale of the coordinates along the genome label. Default value is scale = "bp". Options are:

  • "bp": base pairs.

  • "Kb": kilobase pairs. 1 kilobase pair is equal to 1000 base pairs.

  • "Mb": megabase pairs. 1 megabase pair is equal to 1000000 base pairs.

commas

A logical value indicating whether to include commas in start and stop labels. Default value is commas = TRUE.
sequence

A logical value indicating whether to include sequence information above the label of an x-axis (only at appropriate resolutions).
boxWidth

A numeric value indicating the width of the boxes representing sequence information at appropriate resolutions. Default value is boxWidth = 0.5.
axis

A character value indicating along which axis to add genome label. Sequence information will not be displayed along a y-axis. Default value is axis = "x". Options are:

  • "x": Genome label will be plotted along the x-axis.

  • "y": Genome label will be plotted along the y-axis. This is typically used for a square Hi-C plot made with plotHicSquare.

at

A numeric vector of x-value locations for tick marks.
tcl

A numeric specifying the length of tickmarks as a fraction of text height. Default value is tcl = 0.5.
x

A numeric or unit object specifying genome label x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying genome label y-location. The character value will place the genome label y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
length

A numeric or unit object specifying length of genome label axis.
just

Justification of genome label relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, or length are only given as numerics. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters or digit specifications. See gpar and formatC.

Value

Returns a genomeLabel object containing relevant genomic region, placement, and grob information.

Examples

## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")
library("BSgenome.Hsapiens.UCSC.hg19")

## Create page
pageCreate(width = 5, height = 3, default.units = "inches")

## Plot and place gene track on page
genesPlot <- plotGenes(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19", fill = c("grey", "grey"),
    fontcolor = c("grey", "grey"),
    x = 0.5, y = 0.25, width = 4, height = 1,
    just = c("left", "top"),
    default.units = "inches"
)

## Plot x-axis genome labels at different scales
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    scale = "Mb",
    x = 0.5, y = 1.25, length = 4, just = c("left", "top"),
    default.units = "inches"
)
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    scale = "Kb",
    x = 0.5, y = 1.5, length = 4, just = c("left", "top"),
    default.units = "inches"
)
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    scale = "bp",
    x = 0.5, y = 1.75, length = 4, just = c("left", "top"),
    default.units = "inches"
)

## Plot a different genomic label region, zooming in enough
## to see base pairs
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 1000050,
    assembly = "hg19",
    x = 0.25, y = 2.2, length = 4.5
)
plotGenomeLabel(
    chrom = "chr8",
    chromstart = 1000000, chromend = 1000020,
    assembly = "hg19",
    x = 0, y = 2.6, length = 5
)

## Hide page guides
pageGuideHide()

Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout

Description

Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout

Usage

plotGG(
    plot,
    x,
    y,
    width,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL
)

Arguments

plot

ggplot, gtable, or grob object.
x

A numeric or unit object specifying ggplot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying ggplot y-location. The character value will place the ggplot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying ggplot width.
height

A numeric or unit object specifying ggplot height.
just

Justification of ggplot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.

Value

Returns a pg_gg object containing relevant placement and grob information.

See Also

ggplot

Examples

## Create a plot using ggplot2
library(ggplot2)
p <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))

## Create a page
pageCreate(width = 4, height = 4, default.units = "inches")

## Place ggplot in page
plotGG(
    plot = p, x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"), default.units = "inches"
)

## Add title
plotText(
    label = "mtcars", fontsize = 14, fontface = "bold",
    x = 1, y = 0.35
)

## Hide page guides
pageGuideHide()

Plot a triangular Hi-C interaction matrix in a rectangular format

Description

Plot a triangular Hi-C interaction matrix in a rectangular format

Usage

plotHicRectangle(
    data,
    resolution = "auto",
    zrange = NULL,
    norm = "KR",
    matrix = "observed",
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")),
    colorTrans = "linear",
    flip = FALSE,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    quiet = FALSE
)

Arguments

data

Path to .hic or .(m)cool file as a string or a 3-column dataframe of interaction counts in sparse upper triangular format.
resolution

A numeric specifying the width in basepairs of each pixel. For files, "auto" will attempt to choose a resolution based on the size of the region. For dataframes, "auto" will attempt to detect the resolution the dataframe contains.
zrange

A numeric vector of length 2 specifying the range of interaction scores to plot, where extreme values will be set to the max or min.
norm

Character value specifying hic data normalization method, if giving .hic or .(m)cool file. This value must be found in the .hic or .(m)cool file. Default value is norm = "KR".
matrix

Character value indicating the type of matrix to output for .hic files. Default value is matrix = "observed". Options are:

  • "observed": Observed counts.

  • "oe": Observed/expected counts.

  • "log2oe": Log2 transformed observed/expected counts.

chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
palette

A function describing the color palette to use for representing scale of interaction scores. Default value is palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")).
colorTrans

A string specifying how to scale Hi-C colors. Options are "linear", "log", "log2", or "log10". Default value is colorTrans = "linear".
flip

A logical indicating whether to flip the orientation of the Hi-C matrix over the x-axis. Default value is flip = FALSE.
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying rectangle Hi-C plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying rectangle Hi-C plot y-location. The character value will place the rectangle Hi-C plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying the width of the Hi-C plot rectangle.
height

A numeric or unit object specifying the height of the Hi-C plot rectangle.
just

Justification of rectangle Hi-C plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.

Details

This function is similar is plotHicTriangle but will fill in additional pixels around the the triangular portion of the plot to make a rectangle. The x-axis represents the genomic coordinates and the y-axis corresponds to distance in Hi-C bins.

A rectangle Hi-C plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotHicRectangle(data, chrom,
                    chromstart = NULL, chromend = NULL,
                    x, y, width, height, just = c("left", "top"),
                    default.units = "inches")

This function can also be used to quickly plot an unannotated rectangle Hi-C plot by ignoring plot placement parameters: 

plotHicRectangle(data, chrom,
                    chromstart = NULL, chromend = NULL)

Value

Returns a hicRectangle object containing relevant genomic region, Hi-C data, placement, and grob information.

See Also

readHic, readCool, plotHicTriangle

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 6, height = 3.5, default.units = "inches")

## Plot and place rectangle Hi-C plot
hicPlot <- plotHicRectangle(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28950000, chromend = 29800000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 5, height = 2.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate x-axis genome label
annoGenomeLabel(
    plot = hicPlot, scale = "Kb", x = 0.5, y = 3.03,
    just = c("left", "top")
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot, x = 5.6, y = 0.5,
    width = 0.13, height = 1.5,
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Plot a Hi-C interaction matrix in a square format

Description

Plot a Hi-C interaction matrix in a square format

Usage

plotHicSquare(
    data,
    resolution = "auto",
    zrange = NULL,
    norm = "KR",
    matrix = "observed",
    chrom,
    chromstart = NULL,
    chromend = NULL,
    altchrom = NULL,
    altchromstart = NULL,
    altchromend = NULL,
    assembly = "hg38",
    palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")),
    colorTrans = "linear",
    half = "both",
    yaxisDir = "increase",
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    quiet = FALSE
)

Arguments

data

Path to .hic or .(m)cool file as a string or a 3-column dataframe of interaction counts in sparse upper triangular format.
resolution

A numeric specifying the width in basepairs of each pixel. For files, "auto" will attempt to choose a resolution based on the size of the region. For dataframes, "auto" will attempt to detect the resolution the dataframe contains.
zrange

A numeric vector of length 2 specifying the range of interaction scores to plot, where extreme values will be set to the max or min.
norm

Character value specifying hic data normalization method, if giving .hic or .(m)cool file. This value must be found in the .hic or .(m)cool file. Default value is norm = "KR".
matrix

Character value indicating the type of matrix to output for .hic files. Default value is matrix = "observed". Options are:

  • "observed": Observed counts.

  • "oe": Observed/expected counts.

  • "log2oe": Log2 transformed observed/expected counts.

chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
altchrom

Alternate chromosome for off-diagonal plotting or interchromosomal plotting, as a string.
altchromstart

Alternate chromosome integer start position for off-diagonal plotting or interchromosomal plotting.
altchromend

Alternate chromosome integer end position for off-diagonal plotting or interchromosomal plotting.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
palette

A function describing the color palette to use for representing scale of interaction scores. Default value is palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")).
colorTrans

A string specifying how to scale Hi-C colors. Options are "linear", "log", "log2", or "log10". Default value is colorTrans = "linear".
half

A character value indicating which diagonal regions to plot. For intrachromosomal plotting, options are "both", "top", or "bottom". For off-diagonal or interchromosomal plotting, options are "top" or "bottom". Default value is half = "both".

  • "both": Both diagonal halves.

  • "top": Half above the diagonal.

  • "bottom": Half below the diagonal.

yaxisDir

A string specifying the genomic direction of the y-axis. Options are "increase", where the bottom left corner of the Hi-C map indicates the origin, and "decrease", where the top left corner of the Hi-C map indicates the origin. This will change the direction of the diagonal for intrachromosomal maps. Default value is yaxisDir = "increase".
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying square Hi-C plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying square Hi-C plot y-location. The character value will place the square Hi-C plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying square Hi-C plot width.
height

A numeric or unit object specifying square Hi-C plot height.
just

Justification of square Hi-C plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.

Details

A square Hi-C plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotHicSquare(data, chrom,
                chromstart = NULL, chromend = NULL,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can be used to quickly plot an unannotated square Hi-C plot by ignoring plot placement parameters: 

plotHicSquare(data, chrom,
                chromstart = NULL, chromend = NULL)

Value

Returns a hicSquare object containing relevant genomic region, Hi-C data, placement, and grob information.

See Also

readHic, readCool

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 3, height = 3, default.units = "inches")

## Plot and place Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 2, height = 2,
    just = c("left", "top"),
    default.units = "inches", bg = "black"
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot, x = 2.6, y = 0.5,
    width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Annotate x-axis and y-axis genome labels
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "x",
    x = 0.5, y = 2.53, just = c("left", "top")
)
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", axis = "y",
    x = 0.47, y = 0.5, just = c("right", "top")
)

## Hide page guides
pageGuideHide()

Plot a Hi-C interaction matrix in a triangular format

Description

Plot a Hi-C interaction matrix in a triangular format

Usage

plotHicTriangle(
    data,
    resolution = "auto",
    zrange = NULL,
    norm = "KR",
    matrix = "observed",
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")),
    colorTrans = "linear",
    flip = FALSE,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    quiet = FALSE
)

Arguments

data

Path to .hic or .(m)cool file as a string or a 3-column dataframe of interaction counts in sparse upper triangular format.
resolution

A numeric specifying the width in basepairs of each pixel. For files, "auto" will attempt to choose a resolution based on the size of the region. For dataframes, "auto" will attempt to detect the resolution the dataframe contains.
zrange

A numeric vector of length 2 specifying the range of interaction scores to plot, where extreme values will be set to the max or min.
norm

Character value specifying hic data normalization method, if giving .hic or .(m)cool file. This value must be found in the .hic or .(m)cool file. Default value is norm = "KR".
matrix

Character value indicating the type of matrix to output for .hic files. Default value is matrix = "observed". Options are:

  • "observed": Observed counts.

  • "oe": Observed/expected counts.

  • "log2oe": Log2 transformed observed/expected counts.

chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
palette

A function describing the color palette to use for representing scale of interaction scores. Default value is palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")).
colorTrans

A string specifying how to scale Hi-C colors. Options are "linear", "log", "log2", or "log10". Default value is colorTrans = "linear".
flip

A logical indicating whether to flip the orientation of the Hi-C matrix over the x-axis. Default value is flip = FALSE.
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying triangle Hi-C plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying triangle Hi-C plot y-location. The character value will place the triangle Hi-C plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying the bottom width of the Hi-C plot triangle.
height

A numeric or unit object specifying the height of the Hi-C plot triangle.
just

Justification of triangle Hi-C plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.

Details

In this orientation, the x-axis represents the genomic coordinates and the y-axis corresponds to distance in Hi-C bins.

A triangle Hi-C plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotHicTriangle(data, chrom,
                chromstart = NULL, chromend = NULL,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can also be used to quickly plot an unannotated triangle Hi-C plot by ignoring plot placement parameters: 

plotHicTriangle(data, chrom,
                chromstart = NULL, chromend = NULL)

If height is << 0.5∗width0.5 * width, the top of the triangle will be cropped to the given height.

Value

Returns a hicTriangle object containing relevant genomic region, Hi-C data, placement, and grob information.

See Also

readHic, readCool

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create a page
pageCreate(width = 4, height = 2.5, default.units = "inches")

## Plot and place triangle Hi-C plot
hicPlot <- plotHicTriangle(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 2, y = 0.5, width = 3, height = 1.5,
    just = "top", default.units = "inches"
)

## Annotate x-axis genome label
annoGenomeLabel(
    plot = hicPlot, scale = "Mb", x = 0.5, y = 2.03,
    just = c("left", "top")
)

## Annotate heatmap legend
annoHeatmapLegend(
    plot = hicPlot, x = 3.5, y = 0.5,
    width = 0.13, height = 1.2,
    just = c("right", "top")
)

## Hide page guides
pageGuideHide()

Plot a chromosome ideogram with or without cytobands

Description

Plot a chromosome ideogram with or without cytobands

Usage

plotIdeogram(
    chrom,
    assembly = "hg38",
    data = NULL,
    orientation = "h",
    flip = FALSE,
    showBands = TRUE,
    fill = NULL,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL
)

Arguments

chrom

Chromosome to be plotted, as a string.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
data

Custom cytoband data, as a dataframe with the following columns: "seqnames", "start", "end", "width", "strand", "name", "gieStain".
orientation

Character value indicating the orientation of the ideogram. Default value is orientation = "h". Options are:

  • "v": Vertical ideogram orientation.

  • "h": Horizontal ideogram orientation.

flip

Logical value indicating whether to reverse the start and end positions of the ideogram. If flip = FALSE (default), the ideogram starts at the top/left and ends at the bottom/right. If flip = TRUE, the start and end positions are reversed, meaning the ideogram starts at the bottom/right and ends at the top/left.
showBands

Logical value indicating whether to draw colored cytobands within ideogram. Default value is showBands = TRUE.
fill

(optional) A vector specifying alternate colors for cytoband stains. To change specific gieStain values (i.e. gneg, gpos, etc.) to specific colors, this vector can be named. This vector must have the same number of colors as there are gieStain values for each genome assembly.
x

A numeric or unit object specifying ideogram x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying ideogram y-location. The character value will place the ideogram y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying ideogram width.
height

A numeric or unit object specifying ideogram height.
just

Justification of ideogram relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.

Details

An ideogram can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotIdeogram(chrom,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can also be used to quickly plot an unannotated ideogram by ignoring plot placement parameters: 

plotIdeogram(chrom)

If no data is provided, Giemsa stain band data will first try to fetch UCSC with AnnotationHub. The results are cached for faster access, but these cached items can be deleted. If no internet connection is available and AnnotationHub has not previously cached the data, custom Giemsa stain band data can be loaded with the 'data' parameter.

Value

Returns a ideogram object containing relevant genomic region, placement, and grob information.

See Also

AnnotationHub

Examples

## Load Giemsa stain band information and genomic
## annotation data for hg19 genome assembly
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(AnnotationHub)

## Create page
pageCreate(width = 4.5, height = 1, default.units = "inches")

## Plot and place ideogram
ideogramPlot <- plotIdeogram(
    chrom = "chr2", assembly = "hg19",
    x = 0.25, y = 0.25, width = 4, height = 0.3,
    just = c("left", "top"),
    default.units = "inches"
)

## Plot text
plotText(
    label = "Chromosome 2", fontcolor = "dark grey",
    x = 4.25, y = 0.65, just = "right"
)

## Hide page guides
pageGuideHide()

Plot a legend

Description

Plot a legend

Usage

plotLegend(
    legend,
    fill = NULL,
    pch = NULL,
    lty = NULL,
    orientation = "v",
    title = NULL,
    fontsize = 10,
    border = TRUE,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

legend

A character or expression vector to appear in the legend.
fill

If specified, this argument will produce boxes filled with the specified colors to appear beside the legend text.
pch

The plotting symbols appearing in the legend, as a numeric vector.
lty

The line types for lines appearing in the legend.
orientation

A string specifying legend orientation. Default value is orientation = "v". Options are:

  • "v": Vertical legend orientation.

  • "h": Horizontal legend orientation.

title

A character value giving a title to be placed at the top of the legend.
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 10.
border

Logical value indicating whether to add a border around heatmap legend. Default value is border = TRUE.
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying legend x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying legend y-location. The character value will place the legend y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying legend width.
height

A numeric or unit object specifying legend height.
just

Justification of legend relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a legend object containing relevant placement and grob information.

Examples

## Load BED data
library(plotgardenerData)
data("IMR90_ChIP_CTCF_reads")

## Create page
pageCreate(width = 7.5, height = 4, default.units = "inches")

## Plot a pileup plot, coloring elements by strand
pileupPlot <- plotRanges(
    data = IMR90_ChIP_CTCF_reads, chrom = "chr21",
    chromstart = 29072500, chromend = 29075000,
    assembly = "hg19",
    fill = colorby("strand", palette = 
                colorRampPalette(c("steel blue", "light salmon"))),
    x = 0.5, y = 3.5, width = 6.5, height = 3.5,
    just = c("left", "bottom"),
    default.units = "inches"
)

## Add a legend depicting strand colors
legendPlot <- plotLegend(
    legend = c("- strand", "+ strand"),
    fill = c("steel blue", "light salmon"),
    border = FALSE,
    x = 5, y = 0.5, width = 1.5, height = 0.7,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = pileupPlot, x = 0.5, y = 3.5,
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Plot a Manhattan plot

Description

Plot a Manhattan plot

Usage

plotManhattan(
    data,
    sigVal = 5e-08,
    chrom = NULL,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fill = "black",
    pch = 19,
    cex = 0.25,
    leadSNP = NULL,
    sigLine = FALSE,
    sigCol = NULL,
    trans = "-log10",
    range = NULL,
    yscale_reverse = FALSE,
    space = 0.01,
    bg = NA,
    baseline = FALSE,
    baseline.color = "grey",
    baseline.lwd = 1,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    flip = FALSE,
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

data

Data to be plotted, as a character value specifying a file path of GWAS data, a dataframe, or a GRanges object. Each of these data types must have the following columns:

  • "chrom": Chromosome names. This column must be a character.

  • "pos": Chromosomal position. This column must be an integer or numeric.

  • "p": p-value or similar measure. This column must be numeric. Values will be converted according to the trans parameter.

  • "snp"(optional): SNP name or rsid. This column should be a character.

sigVal

A numeric specifying the significance level of p-values. Along with data p-values, this value will be converted according to the trans parameter. Default value is sigVal = 5e-08.
chrom

Chromosome of region to be plotted, as a string. If left NULL, all chromosomes found in data will be plotted.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
fill

A single character value, a vector, or a colorby object specifying fill colors of data points. For a Manhattan plot with multiple chromosomes, a vector of colors will be used to color points of different chromosomes. Default value is fill = "black".
pch

A numeric value or numeric vector specifying point symbols. If colorby object is supplied for fill, point symbols will be mapped to colorby values. Default value is pch = 19.
cex

A numeric indicating the amount by which points should be scaled relative to the default. Default value is cex = 0.25.
leadSNP

A list specifying the lead SNP in the desired region and any associated aesthetic features of the lead SNP data point and text label. The lead SNP should be specified as a character with the name slot "snp" in the list. Accepted lead SNP aesthetic features in the list include fill, pch, cex, fontcolor, and fontsize.
sigLine

Logical value indicating whether to draw a line at the significance level indicated with sigVal. Default value is sigLine = FALSE.
sigCol

Single character value specifying the color of significant data points.
trans

Character value specifying the transformation to apply to the "p" column plotted along the y-axis. For no transformation, set value to the empty character "". Default value is trans = "-log10".
range

A numeric vector of length 2 specifying the y-range of p-values to plot (c(min, max)).
yscale_reverse

Logical value indicating whether to reverse the y-scale and order points from max to min.
space

A numeric value indicating the space between each chromosome as a fraction of the width of the plot, if plotting multiple chromosomes. Default value is space = 0.01.
bg

Character value indicating background color. Default value is bg = NA.
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = FALSE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
x

A numeric or unit object specifying Manhattan plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying Manhattan plot y-location. The character value will place the Manhattan plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying Manhattan plot width.
height

A numeric or unit object specifying Manhattan plot height.
just

Justification of Manhattan plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
flip

Logical value indicating whether to reflect Manhattan plot over the x-axis. Default value is flip = FALSE.
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Details

A Manhattan plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotManhattan(data,
                chrom = NULL,
                chromstart = NULL, chromend = NULL,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can also be used to quickly plot an unannotated Manhattan plot by ignoring plot placement parameters: 

plotManhattan(data,
                chrom = NULL,
                chromstart = NULL, chromend = NULL)

Value

Returns a manhattan object containing relevant genomic region, placement, and grob information.

Examples

## Load genomic assembly information
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
## Load GWAS data
library(plotgardenerData)
data("hg19_insulin_GWAS")

## Create a page
pageCreate(width = 7.5, height = 4.5, default.units = "inches")

## Plot all GWAS data
manhattanPlot <- plotManhattan(
    data = hg19_insulin_GWAS, assembly = "hg19",
    fill = c("grey", "#37a7db"),
    sigLine = TRUE,
    trans = "-log10",
    col = "grey", lty = 2, range = c(0, 14),
    x = 0.5, y = 0, width = 6.5, height = 2,
    just = c("left", "top"),
    default.units = "inches"
)
## Annotate genome label
annoGenomeLabel(
    plot = manhattanPlot, x = 0.5, y = 2, fontsize = 8,
    just = c("left", "top"),
    default.units = "inches"
)
plotText(
    label = "Chromosome", fontsize = 8,
    x = 3.75, y = 2.20, just = "center", default.units = "inches"
)

## Annotate y-axis
annoYaxis(
    plot = manhattanPlot, at = c(0, 2, 4, 6, 8, 10, 12, 14),
    axisLine = TRUE, fontsize = 8
)

## Plot y-axis label
plotText(
    label = "-log10(p-value)", x = 0.15, y = 1, rot = 90,
    fontsize = 8, fontface = "bold", just = "center",
    default.units = "inches"
)


## Plot GWAS data zooming in on chromosome 11
## highlighting a lead SNP, and coloring by LD score
hg19_insulin_GWAS$LD <- as.numeric(hg19_insulin_GWAS$LD)
## Group LD column into LD ranges
hg19_insulin_GWAS <- as.data.frame(dplyr::group_by(hg19_insulin_GWAS,
                                        LDgrp = cut(
                                        hg19_insulin_GWAS$LD,
                                        c(0, 0.2, 0.4, 0.6, 0.8, 1))))
hg19_insulin_GWAS$LDgrp <- addNA(hg19_insulin_GWAS$LDgrp)
leadSNP_p <- min(hg19_insulin_GWAS[
    which(hg19_insulin_GWAS$chrom == "chr11"), ]$p)
leadSNP <- hg19_insulin_GWAS[which(hg19_insulin_GWAS$p == leadSNP_p), ]$snp
chr11_manhattanPlot <- plotManhattan(
    data = hg19_insulin_GWAS, chrom = "chr11",
    chromstart = 60000000,
    chromend = 130000000,
    assembly = "hg19",
    fill = colorby("LDgrp",
    palette = colorRampPalette(c(
        "#1f4297",
        "#37a7db", "green",
        "orange", "red", "grey"
    ))),
    trans = "-log10",
    sigLine = TRUE, col = "grey",
    lty = 2, range = c(0, 16),
    leadSNP = list(
        snp = leadSNP,
        pch = 18,
        cex = 0.75,
        fill = "#7ecdbb",
        fontsize = 8
    ),
    x = 0.5, y = 2.5, width = 6.5,
    height = 1.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Plot legend for LD scores
plotLegend(
    legend = c(
        "LD Ref Var",
        paste("0.4", ">", "r^2", 
        "", ">=", "0.2"),
        paste("0.2", ">", "r^2", 
        "", ">=", "0"),
        "no LD data"
    ),
    fill = c("#7ecdbb", "#37a7db", "#1f4297", "grey"), cex = 0.75,
    pch = c(18, 19, 19, 19), border = FALSE, x = 7, y = 2.5,
    width = 1.5, height = 0.6, just = c("right", "top"),
    default.units = "inches"
)


## Annotate genome label
annoGenomeLabel(
    plot = chr11_manhattanPlot, x = 0.5, y = 4.01,
    fontsize = 8, scale = "Mb",
    just = c("left", "top"), default.units = "inches"
)

## Annotate y-axis
annoYaxis(
    plot = chr11_manhattanPlot,
    at = c(0, 2, 4, 6, 8, 10, 12, 14, 16),
    axisLine = TRUE, fontsize = 8
)

## Plot y-axis label
plotText(
    label = "-log10(p-value)", x = 0.15, y = 3.25, rot = 90,
    fontsize = 8, fontface = "bold", just = "center",
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

Plot multiple signal tracks in line with each other

Description

Plot multiple signal tracks in line with each other

Usage

plotMultiSignal(
   data,
   binSize = NA, 
   binCap = TRUE, 
   negData = FALSE,
   chrom, 
   chromstart = NULL, 
   chromend = NULL,
   assembly = "hg38", 
   linecolor= "#37a7db",
   fill = NA, 
   ymax = 1, 
   range = NULL, 
   scale = FALSE,
   label = NULL,
   bg = NA, 
   baseline = TRUE, 
   baseline.color = "grey",
   baseline.lwd = 1, 
   orientation = "h", 
   x = NULL, 
   y = NULL,
   width = NULL,
   height = NULL,
   just = c("left", "top"),
   gapdistance = .2,
   default.units = "inches", 
   draw = TRUE,
   params = NULL, ...
)

Arguments

data

List of data to be plotted as character values specifying multiple bigwig file paths, dataframes in BED format, or GRanges objects with metadata column score.
binSize

A numeric specifying the length of each data bin in basepairs. Default value is binSize = NA.
binCap

A logical value indicating whether the function will limit the number of data bins to 8,000. Default value is binCap = TRUE.
negData

A logical value indicating whether any of the data has both positive and negative scores and the y-axis of each signal track should be split. Default value is negData = FALSE.
chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
linecolor

A character value or vector of character values specifying the line color(s) outlining the signal tracks. Default value is linecolor = "#37a7db".
fill

A character value or vector specifying the fill color(s) of the signal tracks. Default value is fill = NA.
ymax

A numeric specifying the fraction of the max y-value to set as the height of each plot. Default value is ymax = 1.
range

A numeric vector of length 2 specifying the y-range of data to plot (c(min, max)) in each signal track. If range = NULL, an optimal range for all signal tracks will be calculated.
scale

A logical value indicating whether to include a data scale label in the top left corner of each plot. Default value is scale = FALSE.
label

An optional character vector to conveniently add text labels to signal tracks. If scale = TRUE, the labels will be drawn in the top right of the signal tracks. Otherwise, the label will be drawn in the top left of the plot. For more customizable labels, use plotText.
bg

Character value indicating background color. Default value is bg = NA.
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = TRUE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
orientation

A string specifying signal track orientations. Default value is orientation = "h". Options are:

  • "v": Vertical signal track orientations, where signal tracks will be stacked from left to right.

  • "h": Horizontal signal track orientations, where signal tracks will be stacked from top to bottom.

x

A numeric vector or unit object specifying the overall multisignal x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying overall multisignal plot y-location. The character value will place the multisignal plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying overall multisignal plot width.
height

A numeric or unit object specifying overall multisignal plot height.
just

Justification of overall multisignal plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
gapdistance

A numeric or unit object specifying space between plots. Default value is gapdistance = 0.2.
default.units

A string indicating the default units to use if x or y are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a list of signal objects containing relevant genomic region, placement, and grob information for each signal track.

Examples

library("plotgardenerData")
data("GM12878_ChIP_CTCF_signal")
data("IMR90_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
data("IMR90_ChIP_H3K27ac_signal")
library("RColorBrewer")

## List of multiple signal datasets
signalList <- list(GM12878_ChIP_CTCF_signal, GM12878_ChIP_H3K27ac_signal, 
    IMR90_ChIP_CTCF_signal, IMR90_ChIP_H3K27ac_signal)

## Create page
pageCreate(width = 6.9, height = 3.5, default.units = "inches")

## Plot multiple signals
multisignal <- plotMultiSignal(signalList, chrom = "chr21",
                               chromstart = 28150000, chromend = 29150000,
                               linecolor = c(brewer.pal(n = 9,"YlGnBu")[4],
                                             brewer.pal(n = 9,"YlGnBu")[5],
                                             brewer.pal(n = 9,"YlGnBu")[6],
                                             brewer.pal(n = 9,"YlGnBu")[7]),
                               label = c("GM12878 CTCF", "GM12878 H3K27ac",
                                         "IMR90 CTCF", "IMR90 H3K27ac"),
                               assembly = "hg19",
                               x = 0.2, y = 0.2,
                               width = 6.5, height = 3,
                               default.units = "inches",
                               gapdistance = 0.1)
                               
## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28150000, chromend = 29150000,
    assembly = "hg19",
    scale = "Kb",
    x = 0.2, y = 3.25, length = 6.5,
    default.units = "inches"
)                                

## Hide page guides
pageGuideHide()

Plot paired-end genomic range elements

Description

Plot paired-end genomic range elements

Usage

plotPairs(
    data,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fill = "#1f4297",
    linecolor = NA,
    bg = NA,
    boxHeight = unit(2, "mm"),
    spaceWidth = 0.02,
    spaceHeight = 0.3,
    limitLabel = TRUE,
    baseline = FALSE,
    baseline.color = "grey",
    baseline.lwd = 1,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

data

A string specifying the BEDPE file path, a dataframe in BEDPE format specifying data to be plotted, or a GInteractions object.
chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
fill

A single character value, a vector, or a colorby object specifying fill colors of paired range elements. Default value is fill = "#1f4297".
linecolor

A single character value, a vector, or a colorby object specifying the color of the lines outlining paired range elements. Default value is linecolor = NA. Special options include:

  • NA: No line color.

  • "fill": Same color as fill.

bg

Character value indicating background color. Default value is bg = NA.
boxHeight

A numeric or unit object specifying height of boxes at either end of paired range elements. Default value is boxHeight = unit(2, "mm").
spaceWidth

A numeric specifying the width of spacing between paired range elements, as a fraction of the plot's genomic range. Default value is spaceWidth = 0.02.
spaceHeight

A numeric specifying the height of space between boxes of paired range elements on different rows. Default value is spaceHeight = 0.3.
limitLabel

A logical value indicating whether to draw a "+" when not all elements can be plotted in the plotting space. Default value is limitLabel = TRUE.
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = FALSE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
x

A numeric or unit object specifying paired range plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying paired range plot y-location. The character value will place the paired range plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying paired range plot width.
height

A numeric or unit object specifying paired range plot height.
just

Justification of paired range plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Details

#' A paired ranges plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotPairs(data, chrom,
            chromstart = NULL, chromend = NULL,
            x, y, width, height, just = c("left", "top"),
            default.units = "inches")

This function can also be used to quickly plot an unannotated paired ranges plot by ignoring plot placement parameters: 

plotPairs(data, chrom,
            chromstart = NULL, chromend = NULL)

Value

Returns a pairs object containing relevant genomic region, placement, and grob information.

Examples

## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Set the coordinates
params <- pgParams(
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    width = 7
)

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Add a length column
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

## Plot the data
bedpePlot <- plotPairs(
    data = IMR90_DNAloops_pairs, params = params,
    fill = colorby("length", palette = 
                colorRampPalette(c("dodgerblue2", "firebrick2"))),
    lwd = 2, spaceHeight = .7,
    x = 0.25, y = 0.25, height = 1.5,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(plot = bedpePlot, x = 0.25, y = 1.78, scale = "Mb")

## Add heatmap legend
annoHeatmapLegend(
    plot = bedpePlot, fontcolor = "black",
    x = 7.0, y = 0.25,
    width = 0.10, height = 1, fontsize = 10
)

## Add heatmap legend label
plotText(
    label = "Kb", rot = 90, x = 6.9, y = 0.75,
    just = c("center", "center"), fontsize = 10
)

## Hide page guides
pageGuideHide()

Plot paired-end genomic range data in an arch style

Description

Plot paired-end genomic range data in an arch style

Usage

plotPairsArches(
    data,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    style = "2D",
    flip = FALSE,
    curvature = 5,
    archHeight = NULL,
    fill = "#1f4297",
    linecolor = NA,
    alpha = 0.4,
    bg = NA,
    clip = FALSE,
    clip.noAnchor = TRUE,
    range = NULL,
    baseline = FALSE,
    baseline.color = "grey",
    baseline.lwd = 1,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

data

A string specifying the BEDPE file path, a dataframe in BEDPE format specifying data to be plotted, or a GInteractions object.
chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
style

Character value describing the style of arches. Default value is style = "2D". Options are:

  • "2D": Arches will be drawn in a 2-dimensional style.

  • "3D": Arches will be drawn in a 3-dimensional style.

flip

Logical value indicating whether to reflect arches over the x-axis. Default value is flip = FALSE.
curvature

Numeric indicating the number of points along the arch curvature. Default value is curvature = 5.
archHeight

Single numeric value, numeric vector, or column name in data specifying the arch heights. When NULL, all arches will be the same height, filling up the given plot area.
fill

A single character value, a vector, or a colorby object specifying fill colors of arches. Default value is fill = #1f4297".
linecolor

A single character value, a vector, or a colorby object specifying the color of the lines outlining arches. Default value is linecolor = NA. Special options include:

  • NA: No line color.

  • "fill": Same color as fill.

alpha

Numeric value specifying transparency. Default value is alpha = 0.4.
bg

Character value indicating background color. Default value is bg = NA.
clip

A logical value indicating whether to clip any arches that get cutoff in the given genomic region. Default value is clip = FALSE.
clip.noAnchor

A logical value indicating whether to clip any arches that overlap the given genomic region but do not have an anchor in that region. Default value is clip.noAnchor = TRUE.
range

A numeric vector of length 2 specifying the y-range of archHeight to plot (c(min, max)).
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = FALSE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
x

A numeric or unit object specifying pair arches plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying BEDPE arches plot y-location. The character value will place the pair arches plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying pair arches plot width.
height

A numeric or unit object specifying pair arches plot height.
just

Justification of pair arches plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Details

A pair arches plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotPairsArches(data chrom,
                chromstart = NULL, chromend = NULL,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can also be used to quickly plot an unannotated pair arches plot by ignoring plot placement parameters: 

plotPairsArches(data, chrom,
                chromstart = NULL, chromend = NULL)

Value

Returns a arches object containing relevant genomic region, placement, and grob information.

Examples

## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Set the coordinates
params <- pgParams(
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    width = 7
)

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Add a length column to color by
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

## Translate lengths into heights
IMR90_DNAloops_pairs$h <- 
        IMR90_DNAloops_pairs$length / max(IMR90_DNAloops_pairs$length)

## Plot the data
archPlot <- plotPairsArches(
    data = IMR90_DNAloops_pairs, params = params,
    fill = colorby("length", palette = 
                colorRampPalette(c("dodgerblue2", "firebrick2"))),
    linecolor = "fill",
    archHeight = "h", alpha = 1,
    x = 0.25, y = 0.25, height = 1.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(plot = archPlot, x = 0.25, y = 1.78, scale = "Mb")


## Annotate heatmap legend
annoHeatmapLegend(
    plot = archPlot, fontcolor = "black",
    x = 7.0, y = 0.25,
    width = 0.10, height = 1, fontsize = 10
)

## Add the heatmap legend title
plotText(
    label = "Kb", rot = 90, x = 6.9, y = 0.75,
    just = c("center", "center"),
    fontsize = 10
)


## Hide page guides
pageGuideHide()

Plot a polygon within a plotgardener layout

Description

Plot a polygon within a plotgardener layout

Usage

plotPolygon(
    x,
    y,
    default.units = "inches",
    linecolor = "black",
    lwd = 1,
    lty = 1,
    fill = NA,
    alpha = 1,
    id = NULL,
    id.lengths = NULL,
    params = NULL,
    ...
)

Arguments

x

A numeric vector or unit object specifying polygon vertex x-locations.
y

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying polygon vertex y-locations. The character vector will place polygon vertex y-locations relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
default.units

A string indicating the default units to use if x or y are only given as numeric vectors. Default value is default.units = "inches".
linecolor

A character value specifying polygon line color. Default value is linecolor = "black".
lwd

A numeric specifying polygon line width. Default value is lwd = 1.
lty

A numeric specifying polygon line type. Default value is lty = 1.
fill

A character value specifying polygon fill color. Default value is fill = NA.
alpha

Numeric value specifying color transparency. Default value is alpha = 1.
id

A numeric vector used to separate locations in x and y into multiple polygons. All locations with the same id belong to the same polygon.
id.lengths

A numeric vector used to separate locations in x and y into multiple polygons. Specifies consecutive blocks of locations which make up separate polygons.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a polygon object containing relevant placement and grob information.

See Also

grid.polygon

Examples

## Create a page
pageCreate(width = 7.5, height = 6, default.units = "inches")

## Plot complex polygons one at a time
plotPolygon(
    x = c(2.6, 4.65, 4.75, 6.05, 1.4, 1.3),
    y = c(2.5, 3.1, 3.5, 4, 3.15, 2.8),
    fill = "#4a168e", linecolor = NA
)

plotPolygon(
    x = c(4.65, 4.75, 6.05, 5.05, 4.4),
    y = c(3.1, 3.5, 4, 1.45, 1.2),
    fill = "#9d28b0", linecolor = NA
)

## Plot multiple triangles with different id's and colors
plotPolygon(
    x = c(
        0.45, 6.05, 3, 3, 6.05, 5.25, 4.4, 5.05, 4.95,
        1.3, 2.6, 1, 4.4, 4.95, 5, 4.95, 5, 6.25
    ),
    y = c(
        2.85, 4, 5.55, 5.55, 4, 5.55, 1.2, 1.45, 1.1,
        2.8, 2.5, 2.1, 1.2, 1.1, 0.45, 1.1, 0.45, 1.1
    ),
    id = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6),
    fill = c(
        "#ce93d9", "#bb6ac9", "#4a168e",
        "#7b1fa0", "#bb6ac9", "#ce93d9"
    ),
    linecolor = NA
)

## Hide page guides
pageGuideHide()

Plot genomic range elements in a pileup or collapsed format

Description

Plot genomic range elements in a pileup or collapsed format

Usage

plotRanges(
    data,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fill = "#7ecdbb",
    linecolor = NA,
    order = "width",
    collapse = FALSE,
    boxHeight = unit(2, "mm"),
    spaceWidth = 0.02,
    spaceHeight = 0.3,
    limitLabel = TRUE,
    strandSplit = FALSE,
    bg = NA,
    baseline = FALSE,
    baseline.color = "grey",
    baseline.lwd = 1,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

data

Data to be plotted; as a character value specifying a BED file path, a data frame in BED format, a character value specifying a .bam file path where a bam index file (.bam.bai) is in the same directory, or a GRanges object.
chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
fill

A single character value, a vector, or a colorby object specifying fill colors of range elements. Default value is fill = "#7ecdbb".
linecolor

A single character value, a vector, or a colorby object specifying the color of the lines outlining range elements. Default value is linecolor = NA. Special options include:

  • NA: No line color.

  • "fill": Same color as fill.

.
order

A character value specifying how to order pileup data before assigning rows. Default value is order = "width". Options include:

  • "width": Ordered by decreasing width of elements.

  • "random": Ordered randomly in each function call.

.
collapse

A logical value indicating whether to collapse range elements into a single row, or into two rows if strandSplit = TRUE. If collapse = TRUE, boxHeight will be ignored and elements will be the height of the entire plot if strandSplit = FALSE or be the height of half of the entire plot if strandSplit = TRUE. Default value is collapse = FALSE.
boxHeight

A numeric or unit object specifying height of range element boxes. Default value is boxHeight = unit(2, "mm").
spaceWidth

A numeric value specifying the width of minimum spacing between range element boxes, as a fraction of the plot's genomic range. Default value is spaceWidth = 0.02.
spaceHeight

A numeric value specifying the height of spacing between range element boxes on different rows, as a fraction of boxHeight. Default value is spaceHeight = 0.3.
limitLabel

A logical value indicating whether to draw a "+" when not all elements can be plotted in the plotting space. Default value is limitLabel = TRUE.
strandSplit

A logical value indicating whether plus and minus-stranded elements should be separated. Elements can only be split by strand if a strand column is found in data. Default value is strandSplit = FALSE.
bg

Character value indicating background color. Default value is bg = NA.
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = FALSE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
x

A numeric or unit object specifying ranges plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying ranges plot y-location. The character value will place the ranges plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying ranges plot width.
height

A numeric or unit object specifying ranges plot height.
just

Justification of ranges plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Details

A ranges plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotRanges(data, chrom,
            chromstart = NULL, chromend = NULL,
            x, y, width, height, just = c("left", "top"),
            default.units = "inches")

This function can also be used to quickly plot an unannotated BED plot by ignoring plot placement parameters: 

plotRanges(data, chrom,
            chromstart = NULL, chromend = NULL)

Value

Returns a ranges object containing relevant genomic region, coloring data, placement, and grob information.

Examples

## Load ranges data in BED format
library(plotgardenerData)
data("IMR90_ChIP_CTCF_reads")

## Create page
pageCreate(width = 7.5, height = 5, default.units = "inches")

## Plot and place a pileup ranges plot
pileupPlot <- plotRanges(
    data = IMR90_ChIP_CTCF_reads, chrom = "chr21",
    chromstart = 29073000, chromend = 29074000,
    assembly = "hg19",
    order = "random",
    fill = colorby("strand", palette = 
                colorRampPalette(c("#7ecdbb", "#37a7db"))),
    strandSplit = TRUE, 
    x = 0.5, y = 0.25, width = 6.5, height = 4.25,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = pileupPlot, x = 0.5, y = 4.5,
    just = c("left", "top")
)

## Add text labels
plotText(
    label = "+ strand", fontcolor = "#37a7db", fontsize = 12,
    x = 0.5, y = 1.25, just = "left"
)
plotText(
    label = "- strand", fontcolor = "#7ecdbb", fontsize = 12,
    x = 0.5, y = 3.5, just = "left"
)

## Hide page guides
pageGuideHide()

Plot a raster object within a plotgardener layout

Description

Plot a raster object within a plotgardener layout

Usage

plotRaster(
    image,
    x,
    y,
    width,
    height,
    just = "center",
    default.units = "inches",
    interpolate = TRUE,
    params = NULL,
    ...
)

Arguments

image

Any R object that can be coerced to a raster object.
x

A numeric vector or unit object specifying raster x-locations.
y

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying raster y-locations. The character vector will place raster y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric vector or unit object specifying raster widths.
height

A numeric vector or unit object specifying raster heights.
just

Justification of text relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = "center".
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics or numeric vectors. Default value is default.units = "inches".
interpolate

A logical value indicating whether to linearly interpolate the image. Default value is interpolate = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a raster object containing relevant placement and grob information.

See Also

grid.raster

Examples

library(png)

## Load images

pg_type <- readPNG(system.file("images",
    "pg-wordmark.png",
    package = "plotgardener"
))

gene_gnome <- readPNG(system.file("images",
    "pg-gnome-hole-shadow.png",
    package = "plotgardener"
))

rlogo <- readPNG(system.file("images", "Rlogo.png", 
                package = "plotgardener"))

## Create page
pageCreate(width = 5, height = 6)

## Plot images
plotRaster(
    image = pg_type,
    x = 2.5, y = 0.25, width = 4, height = 1.5,
    just = "top"
)

plotRaster(
    image = gene_gnome,
    x = 2.5, y = 2.25, width = 3.5, height = 3.5,
    just = "top"
)

plotRaster(
    image = rlogo,
    x = 1, y = 1.5, width = 0.5, height = 0.45,
    just = c("left", "top")
)

## Hide page guies
pageGuideHide()

Plot a rectangle within a plotgardener layout

Description

Plot a rectangle within a plotgardener layout

Usage

plotRect(
    x,
    y,
    width,
    height,
    just = "center",
    default.units = "inches",
    linecolor = "black",
    lwd = 1,
    lty = 1,
    fill = NA,
    alpha = 1,
    params = NULL,
    ...
)

Arguments

x

A numeric vector or unit object specifying rectangle x-locations.
y

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying rectangle y-locations. The character vector will place rectangle y-locations relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric vector or unit object specifying rectangle widths.
height

A numeric vector or unit object specifying rectangle heights.
just

Justification of rectangle relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = "center".
default.units

A string indicating the default units to use if x, y, width, and height are only given as numerics or numeric vectors. Default value is default.units = "inches".
linecolor

A character value specifying rectangle line color. Default value is linecolor = "black".
lwd

A numeric specifying rectangle line width. Default value is lwd = 1.
lty

A numeric specifying rectangle line type. Default value is lty = 1.
fill

A character value specifying rectangle fill color. Default value is fill = NA.
alpha

Numeric value specifying color transparency. Default value is alpha = 1.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a rect object containing relevant placement and grob information.

See Also

grid.rect

Examples

## Create a page
pageCreate(width = 7.5, height = 6, default.units = "inches")

## Plot one rectangle with no fill
plotRect(
    x = 0.5, y = 0.5, width = 3, height = 3,
    just = c("left", "top"), default.units = "inches",
    lwd = 2, fill = NA
)


## Plot two rectangles with same width and height at different locations
plotRect(
    x = 4, y = c(0.5, 2.25), width = 3, height = 1.25,
    just = c("left", "top"), default.units = "inches",
    fill = "#7ecdbb"
)

## Plot two rectangles with different widths, heights,
## locations, and colors
plotRect(
    x = 3.75, y = c(4, 5.25), width = c(6.5, 4.5),
    height = c(1, 0.25),
    just = "top", default.units = "inches",
    fill = c("#7ecdbb", "#37a7db"), linecolor = NA, alpha = 0.4
)

## Hide page guides
pageGuideHide()

Draw a line segment within a plotgardener layout

Description

Draw a line segment within a plotgardener layout

Usage

plotSegments(
    x0,
    y0,
    x1,
    y1,
    default.units = "inches",
    linecolor = "black",
    lwd = 1,
    lty = 1,
    lineend = "butt",
    linejoin = "mitre",
    arrow = NULL,
    params = NULL,
    ...
)

Arguments

x0

A numeric vector or unit object indicating the starting x-values of the line segments.
y0

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying starting y-values of the line segments. The character vector will place starting y-values relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
x1

A numeric vector or unit object indicating the stopping x-values of the line segments.
y1

A numeric vector, unit object, or a character vector of v alues containing a "b" combined with a numeric value specifying stopping y-values of the line segments. The character vector will place stopping y-values relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
default.units

A string indicating the default units to use if x0, y0, x1, or y1 are only given as numeric vectors. Default value is default.units = "inches".
linecolor

A character value specifying segment line color. Default value is linecolor = "black".
lwd

A numeric specifying segment line width. Default value is lwd = 1.
lty

A numeric specifying segment line type. Default value is lty = 1.
lineend

A character value specifying line end style. Default value is lineend = "butt". Options are:

  • "round": Segment ends are rounded.

  • "butt": Segment ends end exactly where ended.

  • "square": Segment ends are squared.

linejoin

A character value specifying line join style. Default value is linejoin = "mitre". Options are:

  • "round": Line joins are rounded.

  • "mitre": Line joins are sharp corners.

  • "bevel": Line joins are flattened corners.

arrow

A list describing arrow heads to place at either end of the line segments, as produced by the arrow function.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a segments object containing relevant placement and grob information.

See Also

grid.segments, arrow

Examples

library(grid)
## Create a page
pageCreate(width = 7.5, height = 6, default.units = "inches")

## Plot one line segment
plotSegments(
    x0 = 3.75, y0 = 0.25, x1 = 3.75, y1 = 5.75,
    default.units = "inches",
    lwd = 3, lty = 2
)

## Plot multiple line segments at different locations in different colors
plotSegments(
    x0 = 0.5, y0 = c(1, 3, 5), x1 = 3.25, y1 = c(1, 3, 5),
    default.units = "inches",
    lwd = 2, linecolor = c("#7ecdbb", "#37a7db", "grey")
)

## Plot a line segment with an arrowhead
plotSegments(
    x0 = 4.5, y0 = 0.5, x1 = 7, y1 = 3,
    default.units = "inches",
    arrow = arrow(type = "closed"), fill = "black"
)

## Plot lines with round lineends
plotSegments(
    x0 = c(4, 7), y0 = 3.5, x1 = 5.5, y1 = 4.5,
    default.units = "inches",
    lwd = 5, lineend = "round"
)

## Hide page guides
pageGuideHide()

Plot any kind of signal track data for a single chromosome

Description

Plot any kind of signal track data for a single chromosome

Usage

plotSignal(
    data,
    binSize = NA,
    binCap = TRUE,
    negData = FALSE,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    linecolor = "#37a7db",
    fill = NA,
    ymax = 1,
    range = NULL,
    scale = FALSE,
    label = NULL,
    bg = NA,
    baseline = TRUE,
    baseline.color = "grey",
    baseline.lwd = 1,
    orientation = "h",
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL,
    ...
)

Arguments

data

Data to be plotted as a character value specifying a bigwig file path, a dataframe in BED format, or a GRanges object with metadata column score. Either one data argument or a list of two can be provided, where the second data will be plotted below the x-axis if positive. The second data can also be negative data.
binSize

A numeric specifying the length of each data bin in basepairs. Default value is binSize = NA.
binCap

A logical value indicating whether the function will limit the number of data bins to 8,000. Default value is binCap = TRUE.
negData

A logical value indicating whether the provided data has negative scores. Default value is negData = FALSE.
chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
linecolor

A character value or vector of length 2 specifying the line color(s) outlining the signal track(s). Default value is linecolor = "#37a7db".
fill

A character value or vector of length 2 specifying the fill color(s) of the signal track(s). Default value is fill = NA.
ymax

A numeric specifying the fraction of the max y-value to set as the height of the plot. Default value is ymax = 1.
range

A numeric vector of length 2 specifying the y-range of data to plot (c(min, max)).
scale

A logical value indicating whether to include a data scale label in the top left corner of the plot. Default value is scale = FALSE.
label

An optional character value to conveniently add a text label to the plot. If scale = TRUE, the label will be draw in the top right of the plot. Otherwise, the label will be drawn in the top left of the plot. For more customizable labels, use plotText. Default value is label = NULL.
bg

Character value indicating background color. Default value is bg = NA.
baseline

Logical value indicating whether to include a baseline along the x-axis. Default value is baseline = TRUE.
baseline.color

Baseline color. Default value is baseline.color = "grey".
baseline.lwd

Baseline line width. Default value is baseline.lwd = 1.
orientation

A string specifying signal track orientation. Default value is orientation = "h". Options are:

  • "v": Vertical signal track orientation.

  • "h": Horizontal signal track orientation.

x

A numeric or unit object specifying signal plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying signal plot y-location. The character value will place the signal plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying signal plot width.
height

A numeric or unit object specifying signal plot height.
just

Justification of signal plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value draw = TRUE.
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Details

#A signal track can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotSignal(data, chrom,
            chromstart = NULL, chromend = NULL,
            x, y, width, height, just = c("left", "top"),
            default.units = "inches")

This function can also be used to quickly plot an unannotated signal track by ignoring plot placement parameters: 

plotSignal(data, chrom,
            chromstart = NULL, chromend = NULL)

Value

Returns a signal object containing relevant genomic region, placement, and grob information.

Examples

## Load signal data
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
data("GM12878_ChIP_H3K27ac_signal")

## Create a page
pageCreate(width = 7.5, height = 2.1, default.units = "inches")

## Define region
region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    range = c(0, 45)
)

## Plot and place signal plots
signal1 <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = region,
    x = 0.5, y = 0.25, width = 6.5, height = 0.65,
    just = c("left", "top"), default.units = "inches"
)

signal2 <- plotSignal(
    data = GM12878_ChIP_H3K27ac_signal, params = region,
    linecolor = "#7ecdbb",
    x = 0.5, y = 1, width = 6.5, height = 0.65,
    just = c("left", "top"), default.units = "inches"
)

## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.68, length = 6.5,
    default.units = "inches"
)

## Add text labels
plotText(
    label = "IMR90", fonsize = 10, fontcolor = "#37a7db",
    x = 0.5, y = 0.25, just = c("left", "top"),
    default.units = "inches"
)
plotText(
    label = "GM12878", fonsize = 10, fontcolor = "#7ecdbb",
    x = 0.5, y = 1, just = c("left", "top"),
    default.units = "inches"
)

## Hide page guides
pageGuideHide()

Plot text within a plotgardener layout

Description

Plot text within a plotgardener layout

Usage

plotText(
    label,
    fontcolor = "black",
    fontsize = 12,
    rot = 0,
    check.overlap = FALSE,
    x,
    y,
    just = "center",
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

label

Character or expression of text to be plotted.
fontcolor

A character value specifying text fontcolor. Default value is fontcolor = "black".
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 12.
rot

A numeric specifying the angle to rotate the text. Default value is rot = 0.
check.overlap

A logical value to indicate whether to check for and omit overlapping text. Default value is check.overlap = FALSE.
x

A numeric vector or unit object specifying text x-location.
y

A numeric vector, unit object, or a character vector of values containing a "b" combined with a numeric value specifying text y-locations. The character vector will place text y-locations relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
just

Justification of text relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = "center".
default.units

A string indicating the default units to use if x or y are only given as numerics or numeric vectors. Default value is default.units = "inches".
params

An optional pgParams object containing relevant function parameters.
...

Additional grid graphical parameters. See gpar.

Value

Returns a text object containing relevant placement and grob information.

See Also

grid.text

Examples

## Create a page
pageCreate(width = 4, height = 2, default.units = "inches")

## Plot text, adjusting fontsize and fontface
plotText(
    label = "plotgardener", fontsize = 14, fontface = "bold",
    x = 1, y = 1, just = "center", default.units = "inches"
)

## Plot text, adjusting color, rotation, and fontfamily
plotText(
    label = "coordinate-based", fontcolor = "#225EA8", rot = 90,
    fontfamily = "HersheyScript", x = 2, y = 1, just = "center",
    default.units = "inches"
)

## Plot a text label in multiple places at once
plotText(
    label = "R", x = c(0.5, 1, 1.5), y = 1.5, just = "center",
    default.units = "inches"
)

## Plot a vector of text labels
plotText(
    label = c("pg", "plot", "gardener"), x = 3, y = c(0.5, 1, 1.75),
    just = "center", default.units = "inches"
)

## Hide page guides
pageGuideHide()

Plot gene transcripts in a pileup style for a single chromosome

Description

Plot gene transcripts in a pileup style for a single chromosome

Usage

plotTranscripts(
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fill = c("#669fd9", "#abcc8e"),
    colorbyStrand = TRUE,
    strandSplit = FALSE,
    boxHeight = unit(2, "mm"),
    spaceWidth = 0.02,
    spaceHeight = 0.3,
    limitLabel = TRUE,
    transcriptHighlights = NULL,
    fontsize = 8,
    labels = "transcript",
    stroke = 0.1,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = NULL,
    just = c("left", "top"),
    default.units = "inches",
    draw = TRUE,
    params = NULL
)

Arguments

chrom

Chromosome of region to be plotted, as a string.
chromstart

Integer start position on chromosome to be plotted.
chromend

Integer end position on chromosome to be plotted.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
fill

Character value(s) as a single value or vector specifying fill colors of transcripts. Default value is fill = c("#669fd9", "#abcc8e").
colorbyStrand

A logical value indicating whether to color plus and minus strands by the first two colors in a fill vector, where plus strand transcripts will be colored by the first fill color and minus strand transcripts will be colored by the second fill color. Default value is colorbyStrand = TRUE.
strandSplit

A logical value indicating whether plus and minus-stranded transcripts should be separated, with plus strand transcripts plotted above the x-axis and minus strand transcripts plotted below the x-axis. Default value is strandSplit = FALSE.
boxHeight

A numeric or unit object specifying height of transcripts. Default value is boxHeight = unit(2, "mm").
spaceWidth

A numeric value specifying the width of minimum spacing between transcripts, as a fraction of the plot's genomic range. Default value is spaceWidth = 0.02.
spaceHeight

A numeric value specifying the height of spacing between transcripts on different rows, as a fraction of boxHeight. Default value is spaceHeight = 0.3.
limitLabel

A logical value indicating whether to draw a "+" when not all elements can be plotted in the plotting space. Default value is limitLabel = TRUE.
transcriptHighlights

A two-column dataframe with a column named "transcript" or "gene" containing transcript names or their associated gene names as strings to highlight and a column named "color" containing corresponding highlight colors.
fontsize

A numeric specifying text fontsize in points. Default value is fontsize = 8.
labels

A character value describing the format of transcript text labels. Default value is labels = "trancript". Options are:

  • NULL: No labels.

  • "transcript": Transcript name labels.

  • "gene": Gene name labels.

  • "both": Combined transcript and gene name labels with the format "gene name:transcript name".

stroke

A numeric value indicating the stroke width for transcript body outlines. Default value is stroke = 0.1.
bg

Character value indicating background color. Default value is bg = NA.
x

A numeric or unit object specifying transcript plot x-location.
y

A numeric, unit object, or character containing a "b" combined with a numeric value specifying transcript plot y-location. The character value will place the transcript plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
width

A numeric or unit object specifying transcript plot width.
height

A numeric or unit object specifying transcript plot height.
just

Justification of transcript plot relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". Default value is just = c("left", "top").
default.units

A string indicating the default units to use if x, y, width, or height are only given as numerics. Default value is default.units = "inches".
draw

A logical value indicating whether graphics output should be produced. Default value is draw = TRUE.
params

An optional pgParams object containing relevant function parameters.

Details

A transcripts plot can be placed on a plotgardener coordinate page by providing plot placement parameters: 

plotTranscripts(chrom, chromstart = NULL, chromend = NULL,
                x, y, width, height, just = c("left", "top"),
                default.units = "inches")

This function can also be used to quickly plot an unannotated transcripts plot by ignoring plot placement parameters: 

plotTranscripts(chrom, chromstart = NULL, chromend = NULL)

Genomic annotation information is acquired through TxDb and OrgDb-class packages, as determined through the assembly parameter.

Value

Returns a transcripts object containing relevant genomic region, placement, and grob information.

See Also

assembly, genomes, defaultPackages

Examples

## Load hg19 genomic annotation packages
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
library("org.Hs.eg.db")

## Create page
pageCreate(width = 7.5, height = 3.5, default.units = "inches")

## Plot and place transcripts
plotTranscripts(
    chrom = "chr8", chromstart = 1000000, chromend = 2000000,
    assembly = "hg19", labels = "gene",
    x = 0.5, y = 0.5, width = 6.5, height = 2.5,
    just = c("left", "top"), default.units = "inches"
)

## Plot genome label
plotGenomeLabel(
    chrom = "chr8", chromstart = 1000000, chromend = 2000000,
    assembly = "hg19",
    x = 0.5, y = 3.03, length = 6.5, default.units = "inches"
)

## Plot a legend
plotLegend(
    legend = c("+ strand", "- strand"),
    fill = c("#669fd9", "#abcc8e"), border = FALSE,
    x = 0.5, y = 1, width = 1, height = 0.5,
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

Read a bigWig file and return it as a data frame

Description

Read a bigWig file and return it as a data frame

Usage

readBigwig(
    file,
    chrom = NULL,
    chromstart = 1,
    chromend = .Machine$integer.max,
    strand = "*",
    params = NULL
)

Arguments

file

A character value specifying the path to the bigwig file.
chrom

Chromosome of data as a string, if data for a specific chromosome is desired.
chromstart

Integer start position on chromosome.
chromend

Integer end position on chromosome.
strand

A character value specifying strand. Default value is strand = "*". Options are:

  • "+": Plus strand.

  • "-": Minus strand.

  • "*": Plus and minus strands.

params

An optional pgParams object containing relevant function parameters.

Details

This function does not work on Windows.

Value

Returns a 6-column dataframe of bigwig information.

See Also

import.bw

Examples

if (.Platform$OS.type != "windows"){
    bwFile <- system.file("extdata/test.bw", package="plotgardenerData")

    ## Read in entire file
    bwData <- readBigwig(file = bwFile)

    ## Read in specified region
    bwRegion <- readBigwig(file = bwFile,
                            chrom = "chr2",
                            chromstart = 1,
                            chromend = 1500)
}

Read a .(m)cool file and return Hi-C data as a dataframe

Description

Read a .(m)cool file and return Hi-C data as a dataframe

Usage

readCool(
    file,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    altchrom = NULL,
    altchromstart = NULL,
    altchromend = NULL,
    resolution = "auto",
    zrange = NULL,
    norm = "NONE",
    binChunkSize = 5e6,
    params = NULL,
    quiet = FALSE
)

Arguments

file

A character value specifying the path to the .(m)cool file.
chrom

Chromosome of data, as a string.
chromstart

Integer start position on chromosome.
chromend

Integer end position on chromosome.
altchrom

Alternate chromosome for interchromosomal data, as a string.
altchromstart

Alternate chromosome integer start position for interchromosomal data.
altchromend

Alternate chromosome integer end position for interchromosomal data.
resolution

A numeric specifying the width of each pixel. "auto" will attempt to choose a resolution in basepairs based on the size of the region.
zrange

A numeric vector of length 2 specifying the range of interaction scores, where extreme values will be set to the max or min.
norm

Character value specifying hic data normalization method. This value must be found in the .(m)cool file. Default value is norm = "NONE".
binChunkSize

A numeric specifying the number of bin indices to read from a file for a given region at a given resolution. If the total amount of data is larger than the binChunkSize, data will be read in multiple chunks. Default value is binChunkSize = 5e6.
params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.

Value

Returns a 3-column dataframe in sparse upper triangular format with the following columns: chrom, altchrom, counts.

Author(s)

Sarah Parker, Nicole Kramer

See Also

readHic

Examples

## .cool file
coolFile <- file.path(tempdir(), "Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool")
download.file(url = "https://usgs2.osn.mghpcc.org/cooler01/examples/hg19/Rao2014-IMR90-MboI-allreps-filtered.1000kb.cool",
    destfile = coolFile)

## Read in region `chr2:10000000-22000000` at 1000Kb cool file resolution
coolData <- readCool(file = coolFile, chrom = "chr2", chromstart = 10000000,
                     chromend = 22000000,
                     resolution = 1000000)

## .mcool file
mcoolFile <- file.path(tempdir(), "LEUK_HEK_PJA27_inter_30.mcool")
download.file(url = "https://zenodo.org/records/10906240/files/LEUK_HEK_PJA27_inter_30.mcool?download=1",
    destfile = mcoolFile)

## Read in region `chr2:1000000-5000000` at 100Kb resolution
mcoolData_100Kb <- readCool(file = mcoolFile, chrom = "2",
                            chromstart = 1000000, chromend = 5000000,
                            resolution = 100000)

## Read in data for chr2 at 2500Kb resolution 
mcoolData_2500Kb <- readCool(file = mcoolFile, chrom = "2",
                             resolution = 2500000)

Read basepair resolutions from an .(m)cool file

Description

Read basepair resolutions from an .(m)cool file

Usage

readCoolBpResolutions(file)

Arguments

file

A character value specifying the path to the .(m)cool file

Value

Vector of basepair resolutions

Author(s)

Sarah Parker

Read chromosomes included in .(m)cool files

Description

Read chromosomes included in .(m)cool files

Usage

readCoolChroms(file, resolution = NULL)

Arguments

file

A character value specifying the path to the .(m)cool file
resolution

optional, specify which resolution(s) to read chromosomes from. Default is all resolutions in 'file'.

Value

Data frame or list of data frames of chromosome names and lengths

Author(s)

Sarah Parker, Nicole Kramer

Read normalizations included in .(m)cool files

Description

Read normalizations included in .(m)cool files

Usage

readCoolNorms(file, resolution = NULL)

Arguments

file

A character value specifying the path to the .(m)cool file
resolution

optional, specify which resolution(s) to read normalization types from. Default is all resolutions in 'file'.

Details

The "BALANCE" normalization refers to applying the pre-calculated matrix balancing weights in the 'weight' dataset of 'file', typically present in files created using cooler. VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR is Knight-Ruiz normalization.

Please note that if using a file from HiC-Pro, ICE normalizations will come from files stored in a separate folder, and thus will not contain any normalizations explicitly called "ICE" or "BALANCE" since values are included already normalized. This normalization can be specified as "NONE".

Value

A vector or list of vectors of available normalizations

Author(s)

Sarah Parker, Nicole Kramer

Read a .hic file and return Hi-C data as a dataframe

Description

Read a .hic file and return Hi-C data as a dataframe

Usage

readHic(
    file,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    altchrom = NULL,
    altchromstart = NULL,
    altchromend = NULL,
    assembly = "hg38",
    resolution = "auto",
    res_scale = "BP",
    zrange = NULL,
    norm = "KR",
    matrix = "observed",
    params = NULL,
    quiet = FALSE
)

Arguments

file

A character value specifying the path to the .hic file.
chrom

Chromosome of data, as a string.
chromstart

Integer start position on chromosome.
chromend

Integer end position on chromosome.
altchrom

Alternate chromosome for interchromosomal data, as a string.
altchromstart

Alternate chromosome integer start position for interchromosomal data.
altchromend

Alternate chromosome integer end position for interchromosomal data.
assembly

Default genome assembly as a string or a assembly object. Default value is assembly = "hg38".
resolution

A numeric specifying the width of each pixel. "auto" will attempt to choose a resolution in basepairs based on the size of the region.
res_scale

A character value specifying the resolution scale. Default value is res_scale = "BP". Options are:

  • "BP": Base pairs.

  • "FRAG": Fragments.

zrange

A numeric vector of length 2 specifying the range of interaction scores, where extreme values will be set to the max or min.
norm

Character value specifying hic data normalization method. This value must be found in the .hic file. Default value is norm = "KR".
matrix

Character value indicating the type of matrix to output. Default value is matrix = "observed". Options are:

  • "observed": Observed counts.

  • "oe": Observed/expected counts.

  • "log2oe": Log2 transformed observed/expected counts.

params

An optional pgParams object containing relevant function parameters.
quiet

A logical indicating whether or not to print messages.

Value

Returns a 3-column dataframe in sparse upper triangular format with the following columns: chrom, altchrom, counts.

See Also

straw

Examples

hicFile <- system.file("extdata/test_chr22.hic", package="plotgardenerData")

## Read in data for all chr22 file at 2.5Mb bp resolution
hicData <- readHic(file = hicFile, chrom = "22",
                    assembly = "hg19",
                    resolution = 2500000) 
                        
## Read in region `chr22:20000000-47500000` at 100 Kb resolution
hicData10Kb <- readHic(file = hicFile, chrom = "22",
                        chromstart = 20000000, chromend = 47500000,
                        assembly = "hg19",
                        resolution = 100000)