Question: Is it possible to visualize ChIP peaks of three different samples in one plot using ChIPseeker?
gravatar for swadha
12 days ago by
University of California, United States
swadha10 wrote:


I used MACS2 to call the peaks of three different ChIP samples. I have 3-bed files which I want to visualize.

I am trying to generate "Average Profile of ChIP peaks binding to TSS region" plot from ChIPseeker. Though I am able to generate three different "Average Profile of ChIP peaks binding to TSS region" plots for each bed file but, I want to generate one figure with will be having peaks of 3 bed files. In short I wanted to merge my three plots in one PNG.

I want to generate something like this:

Any kind of help will be great. looking forward to hearing back from you. Thanks in advance Swadha

chipseeker chip-seq bdg • 126 views
ADD COMMENTlink modified 9 days ago by ZZzzzzhong90 • written 12 days ago by swadha10

well HOMER has everything what you need. merge peaks from all the files and calculate enrichment over merged files.

ADD REPLYlink modified 12 days ago • written 12 days ago by prakash510

Thanks for getting back. I will definitely look into HOMER's kit

ADD REPLYlink written 12 days ago by swadha10
gravatar for ZZzzzzhong
9 days ago by
ZZzzzzhong90 wrote:

This is easy to implement by CHIPseeker. Let's say 1_peak,2_peak and 3_peak are your peak_file.

files <- list(1_peak,2_peak,3_peak)
peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb,tssRegion=c(-3000, 3000), verbose=FALSE)
plotDistToTSS(peakAnnoList) + theme(plot.title = element_text(hjust = 0.5))

Then you will get the picture you want.

ADD COMMENTlink written 9 days ago by ZZzzzzhong90

Thanks for getting back. Yes, I got the desired output. I am able to plot all the graphs in one plot. I have one more small question. How do I change the legends? By default, it labels the graphs as "peak1" peak2" peak3" and so forth. How do change the labels?

ADD REPLYlink written 8 days ago by swadha10

if you want to label 1_peak as name1(Any name you want) you can do thatfiles <- list(name1=1_peak,name2=2_peak,name3=3_peak)

ADD REPLYlink written 8 days ago by ZZzzzzhong90
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