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YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
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Feature requests about plotPeakProf2 #189

Open yuanlizhanshi opened 2 years ago

yuanlizhanshi commented 2 years ago

Could it be possible to support more genomic regions by plotPeakProf2?

Now the by parameter of plotPeakProf2 is only support one of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR' .

Could it be possible to support two or more regions, such as UTR regions, which means 3UTR + 5UTR

Could it be possible to support custom genome regions, such as the insulator or enhancer? which could be very helpful in histone modification (H3K4me1).

l will be appreciated it if you could take my requests into consideration

GuangchuangYu commented 2 years ago

I think this can be supported by allowing users to provide regions of interest via a GRanges object.

yuanlizhanshi commented 2 years ago

Thank you for your commitment.

These new features satisfied my requests perfectly.

yuanlizhanshi commented 2 years ago

Hello, I have used some of the new features of plotPeakProf2.

It could be able to compare the peak distribution in self-made Grange objects such as the enhancers region.

But if it could accept two or more self-made Grange objects in plotPeakProf2 would be better.

Thus, we could divide our genes into different groups by their expression levels or other interest features to compare wheater TF is correlated to gene expression. Besides, we also could compare the H3K4me1 peak distribution in enhancer regions or non-enhancer regions.

l will be appreciated it if you could take my requests into consideration