R: Calculate and add genomic density track

circos.genomicDensity {circlize}

R Documentation

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,
    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`
`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.

References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

Examples

## Not run: 

load(system.file(package = "circlize", "extdata", "DMR.RData"))

# rainfall
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()


## End(Not run)

[Package circlize version 0.4.1 Index]