Question: 2 peak files in plotAvgProf2 [ChIPseeker]
0
gravatar for anu014
4 months ago by
anu014160
India
anu014160 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 4 months ago by zx87546.5k • written 4 months ago by anu014160
1

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 4 months ago • written 4 months ago by jared.andrews071.8k

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

ADD REPLYlink modified 3 months ago • written 3 months ago by anu014160
3
gravatar for ZZzzzzhong
4 months ago by
ZZzzzzhong190
ZZzzzzhong190 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 4 months ago by ZZzzzzhong190

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 3 months ago by anu014160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1339 users visited in the last hour