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plotProfile couldn't generate the heatmap with right color

I am trying to use plotProfile to plot a gene-wise profile for a large peak set: show the upstream of the gene, gene body, and downstream of the gene. However the heatmap I generated is never right. Here is the command I used:

computeMatrix scale-regions -S peakSet_expr.bw -R Homo_sapiens.GRCh38.89.gtf -b 3000 -a 3000 -o peakSet_expr_default.gz -p 8

plotProfile -m peakSet_expr_default.gz --plotType heatmap -out peakSet_expr_default.pdf

The figure I got:

enter image description here

deeptools
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written by Tongjun • Tongjun

Have you looked into using plotHeatmap instead of plotProfile?

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written by Trivas • Trivas

I actually tried the plotHeatmap first, but it generated an even weird figure. Here is the command:

plotHeatmap -m peakSet_expr_default.gz -out peakSet_expr_default.png --colorMap RdBu

And the figure is black: enter image description here

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written by Tongjun • Tongjun

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