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How to annotate a region in Heatmap? #1316

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4 tasks done
li1311139481 opened this issue Jul 4, 2024 · 0 comments
Open
4 tasks done

How to annotate a region in Heatmap? #1316

li1311139481 opened this issue Jul 4, 2024 · 0 comments

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@li1311139481
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li1311139481 commented Jul 4, 2024

Welcome to deepTools GitHub repository! Before opening the issue please check
that the following requirements are met :

  • Search whether this issue (or a similar issue) has been solved before
    using the search tab above. Link the previous issue if appropriate below.

  • Paste your deepTools version (deeptools --version) and your python
    version (python --version) below.
    deeptools 3.5.5
    Python 3.10.12

  • Paste the full deepTools command that produces the issue below
    (ignore if you simply spotted the issue in the code/documentation).

/cluster/facility/hlhuang/miniconda3/envs/pip/bin/computeMatrix reference-point --referencePoint center -p ${THREADS} -b 3000 -a 3000 -R "/cluster/facility/hlhuang/zifeng001/1file/ATACregion/tss.bed" -S bigwig/*.bw --skipZeros -o tss/TSS.gz  
/cluster/facility/hlhuang/miniconda3/envs/pip/bin/plotHeatmap -m tss/TSS.gz  -out tss/TSS_Heatmap.pdf --plotFileFormat pdf  --dpi 720
  • Paste the output printed on screen from the command that produces the issue
    below (ignore if you simply spotted the issue in the code/documentation).
    image

Question:
I get the result. but i want anno the heatmap using some gene. As you can see, my input is differential peaks or Tss.bed, and i annotate the peaks to gene, Or I want to know which gene's TSS is different in different samples. I know featureAlignedHeatmap function in ChIPpeakAnno package in R. But I don't think it's clear enough, especially when it's presented as anno_block.

I want annotate the region in heatmap like this
image

Any help would be appreciated

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