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 0.4.5 Index]