annoDomains: Annotate domains in a Hi-C plot

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

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()

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