problem with plotheatmap colors

Question

[alanlongjiao]

Hello, I'm having some trouble with making heatmaps from deeptools, where the colors don't seem to be displayed properly. I would like to make metagene plots using bigwig files from a chip-seq experiment. When I generate the bigwig files using bamCompare, the downstream heatmaps look fine; but if I use bamCoverage, most of the heatmap tends to be white (see attached image for an example). Playing with zMin zMax doesn't seem to help.

Any suggestions would be greatly appreciated~! Thanks!

Alan

[Ram]

Please show us the code you're using to generate these heatmaps.

[alanlongjiao]

Right, sorry. And thanks for replying!

#bamCompare at genes: 
computeMatrix scale-regions \
--scoreFileName $bwDir/DMSO-IP.merge.bamCompare.bw $bwDir/250nM-IP.merge.bamCompare.bw $bwDir/500nM-IP.merge.bamCompare.bw  \
--regionsFileName $genes.bed \
--blackListFileName $blacklist_hg38 \
-o bamCompare.mat.gz \
--beforeRegionStartLength 1000 \
--afterRegionStartLength 1000 \
--sortRegions descend \
--sortUsing mean \
--binSize 5 \
-p 6 
plotHeatmap -m bamCompare.mat.gz \
-o bamCompare.png \
--heatmapHeight 12 \
--heatmapWidth 4 \
--samplesLabel "DMSO" "250nM" "500nM" \
--yAxisLabel "Enrichment over Input" \
--missingDataColor 1 \
--perGroup

#bamCoverage (IP) at genes: 
computeMatrix scale-regions \
--scoreFileName $bwDir/DMSO-IP.merge.bamCoverage.bw $bwDir/250nM-IP.merge.bamCoverage.bw $bwDir/500nM-IP.merge.bamCoverage.bw  \
--regionsFileName $genes.bed \
--blackListFileName $blacklist_hg38 \
-o bamCompare.mat.gz \
--beforeRegionStartLength 1000 \
--afterRegionStartLength 1000 \
--sortRegions descend \
--sortUsing mean \
--binSize 5 \
-p 6 
plotHeatmap -m bamCoverage.mat.gz \
-o bamCoverage.png \
--heatmapHeight 12 \
--heatmapWidth 4 \
--samplesLabel "DMSO" "250nM" "500nM" \
--yAxisLabel "Enrichment over Input" \
--missingDataColor 1 \
--perGroup

Answer 1

[alanlongjiao]

Actually I realized the problem was in the bamCoverage step to generate the bigwigs. If I just remove the --skipNAs option, the resulting bigwigs produce heatmaps that look more like what I would expect.

[Ram]

I've moved your comment to an answer. Please accept it to mark the post as resolved.