2 peak files in plotAvgProf2 [ChIPseeker]
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2.5 years ago
anu014 ▴ 180

Hello Biostars!,

Can someone tell me how to plot 2 peak files in a single plot using plotAvgProf2. I was using below command but it gave me just one sample:

plotAvgProf2(c(peak2,peak3), TxDb=txdb, upstream=3000, downstream=3000,weightCol="fold_enrichment", xlab="Genomic Region (5'->3')", ylab = "Read Count Frequency"


Thanks :)

ChIP-Seq R ChIPseeker Bioconductor • 1.3k views
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I think the peak files need to be passed in as a list.

Also, be sure to recognize that all of ChIPSeeker's average peak profiles just show the number/frequency of peaks, not the number of reads. The vignette is slightly confusing in that regarding since all of the y-axis labels are "Read Count Frequency", though that's not really what's being shown.

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Thanks a lot for this information! ACTUALLY, I was thinking that it's read count only..

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Hi, Do you think average plot over "peak count frequency" compare to other method like deeptools plot over "normalized read depth", which one is more informative?

Thank you!

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Personally, I find the latter much more generally informative, but it depends on what you're trying to show.

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2.5 years ago
ZZzzzzhong ▴ 210
files <- list(peak2,peak3)
promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
tagMatrixList <- lapply(files, getTagMatrix, windows=promoter)
plotAvgProf(tagMatrixList, xlim=c(-3000, 3000))

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Thanks a lot ! It was really helpful. Can you tell me how to change the colors of the samples in the plot? It's always giving me blue n brown color as default..