Entering edit mode
21 months ago
Tongjun
•
0
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:
Have you looked into using plotHeatmap instead of plotProfile?
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: