plotPairs: Plot paired-end genomic range elements

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

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()

PhanstielLab/BentoBox documentation built on June 30, 2024, 12:50 p.m.