annoPixels: Annotate pixels in a Hi-C plot

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

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()

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