plotHicSquare: Plot a Hi-C interaction matrix in a square format

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

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 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 hic 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 file. 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.
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

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()

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