annoPixels {plotgardener} | R Documentation

## Annotate pixels in a Hi-C plot

### Description

Annotate pixels in a Hi-C plot

### Usage

    annoPixels(
        plot,
        data,
        type = "box",
        half = "inherit",
        shift = 4,
        params = NULL,
        quiet = FALSE,
        ...
    )

### Arguments

`plot` | Hi-C plot object from `plotHicSquare` or `plotHicTriangle` on which to annotate pixels.
`data` | A string specifying the BEDPE file path, a dataframe in BEDPE format specifying pixel positions, or a GInteractions object specifying pixel positions.
`type` | Character value specifying type of annotation. Default value is `type = "box"`. Options are: `"box"`: Boxes are drawn around each pixel. `"circle"`: Circles are drawn around each pixel. `"arrow"`: Arrows are drawn pointing to each pixel.
`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"`: Pixels will be annotated on the `half` inherited by the input Hi-C plot. `"both"`: Pixels will be annotated on both halves of the diagonal of a square Hi-C plot. `"top"`: Pixels will be annotated on the upper diagonal half of a square Hi-C plot. `"bottom"`: Pixels will be annotated on the bottom diagonal half of a square Hi-C plot.
`shift` | Numeric specifying the number of pixels on either end of main pixel in a box or circle. Numeric specifying number of pixels for the length of an arrow.
`params` | An optional pgParams object containing relevant function parameters.
`quiet` | A logical indicating whether or not to print messages.
`...` | Additional grid graphical parameters. See gpar.

### Value

Returns a `pixel` object containing relevant genomic region, placement, and grob information.

### Examples

    ## Load Hi-C data and BEDPE data
    library(plotgardenerData)
    data("IMR90_HiC_10kb")
    data("IMR90_DNAloops_pairs")

    ## 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 loops of both sides of Hi-C plot with squares
    pixels <- annoPixels(
        plot = hicPlot, data = IMR90_DNAloops_pairs, type = "box",
        half = "both"
    )

    ## Annotate loops on one side of Hi-C plot with arrows
    ## and the other side with circles
    pagePlotRemove(plot = pixels)
    pixels1 <- annoPixels(
        plot = hicPlot, data = IMR90_DNAloops_pairs,
        type = "arrow", half = "top", shift = 8
    )
    pixels2 <- annoPixels(
        plot = hicPlot, data = IMR90_DNAloops_pairs,
        type = "circle", half = "bottom"
    )

    ## 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]