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To answer the issue, I extend the covplot function to support viewing coverage of a list of GRanges objects or bed files.
library(ChIPseeker)
files <- getSampleFiles()
peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[[4]]),
CBX7=readPeakFile(files[[5]]))
p <- covplot(peak)
print(p)
By default, The coverage plot are merged together with different color. Users can separate them to different panels using facet_grid.
library(ggplot2) col <- c(CBX6='red', CBX7='green') p + facet_grid(chr ~ .id) + scale_color_manual(values=col) + scale_fill_manual(values=col)
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