circos.genomicDensity: Calculate and add genomic density track

In 1156054203/circlize-: Circular Visualization

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)

1156054203/circlize- documentation built on May 22, 2019, 2 p.m.