circlize (version 0.4.10)

circos.genomicDensity: Calculate and add genomic density track

Description

Calculate and add genomic density track

Usage

circos.genomicDensity(
    data,
    ylim.force = FALSE,
    window.size = NULL,
    overlap = TRUE,
    count_by = c("percent", "number"),
    col = ifelse(area, "grey", "black"),
    lwd = par("lwd"),
    lty = par("lty"),
    type = "l",
    area = TRUE,
    area.baseline = NULL,
    baseline = 0,
    border = NA,
    ...)

Arguments

data

A bed-file-like data frame or a list of data frames

ylim.force

Whether to force upper bound of ylim to be 1.

window.size

Pass to genomicDensity

overlap

Pass to genomicDensity

count_by

Pass to genomicDensity

col

Colors. It should be length of one. If data is a list of data frames, the length of col can also be the length of the list.

lwd

Width of lines

lty

Style of lines

type

Type of lines, see circos.lines

area

See circos.lines

area.baseline

Deprecated, use baseline instead.

baseline

See circos.lines

border

See circos.lines

...

Pass to circos.trackPlotRegion

Details

This function is a high-level graphical function, and it will create a new track.

See Also

https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-density-and-rainfall-plot

Examples

# NOT RUN {
load(system.file(package = "circlize", "extdata", "DMR.RData"))

# rainfall
# }
# NOT RUN {
circos.initializeWithIdeogram(plotType = c("axis", "labels"))

bed_list = list(DMR_hyper, DMR_hypo)
circos.genomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))

circos.genomicDensity(bed_list[[1]], col = c("#FF000080"), track.height = 0.1)
circos.genomicDensity(bed_list[[2]], col = c("#0000FF80"), track.height = 0.1)

circos.clear()
# }