Question: 2 peak files in plotAvgProf2 [ChIPseeker]
gravatar for anu014
17 months ago by
anu014170 wrote:

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 :)

ADD COMMENTlink modified 17 months ago by zx87549.1k • written 17 months ago by anu014170

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.

ADD REPLYlink modified 17 months ago • written 17 months ago by jared.andrews075.2k

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

ADD REPLYlink modified 16 months ago • written 16 months ago by anu014170

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!

ADD REPLYlink written 7 months ago by Jingyue30

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

ADD REPLYlink written 7 months ago by jared.andrews075.2k
gravatar for ZZzzzzhong
17 months ago by
ZZzzzzhong210 wrote:
files <- list(peak2,peak3)
promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
tagMatrixList <- lapply(files, getTagMatrix, windows=promoter)
plotAvgProf(tagMatrixList, xlim=c(-3000, 3000))
ADD COMMENTlink written 17 months ago by ZZzzzzhong210

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..

ADD REPLYlink written 16 months ago by anu014170
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