plotPairsArches: Plot paired-end genomic range data in an arch style

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

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()

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