annoDomains {plotgardener} | R Documentation

## 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()

[Package plotgardener version 1.0.17 Index]