2 peak files in plotAvgProf2 [ChIPseeker]

Question

[anu014]

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"

Please help me out..

Thanks :)

[jared.andrews07]

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.

[anu014]

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

[Jingyue]

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!

[jared.andrews07]

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

Answer 1

[ZZzzzzhong]

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

[anu014]

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..