Question: Is it possible to visualize ChIP peaks of three different samples in one plot using ChIPseeker?
0
gravatar for s.singh
21 months ago by
s.singh20
University of California, United States
s.singh20 wrote:

Hi,

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: https://drive.google.com/file/d/1uGscEzuqmASboDLABGI2TcDdIWw3-b5B/view?usp=sharing

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

chipseeker chip-seq bdg • 1.2k views
ADD COMMENTlink modified 21 months ago by ZZzzzzhong210 • written 21 months ago by s.singh20
1

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

ADD REPLYlink modified 21 months ago • written 21 months ago by Prakash1.9k

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

ADD REPLYlink written 21 months ago by s.singh20
4
gravatar for ZZzzzzhong
21 months ago by
ZZzzzzhong210
ZZzzzzhong210 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 21 months ago by ZZzzzzhong210

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 21 months ago by s.singh20
1

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 21 months ago by ZZzzzzhong210

It is working now! Thank you!

ADD REPLYlink written 21 months ago by s.singh20
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