PlotHeatmap in deeptools horizontally

Question

[minoo]

I am using deeptools to draw genomics heatmap with using two bed files and one bigwig file. But it draws heatmap vertically instead of horizontally. So one of the heatmaps is always compressed with short length. Anyone know how to fix this? I need to draw heatmaps horizontally, next to each other. I am using the code below:

computeMatrix reference-point --referencePoint center \
  -b 1000 -a 1000 \
  -R p1.bed p2.bed \
  -S b1.bw \
  --skipZeros \
  -o R1.gz \
  -p 6 \
  --missingDataAsZero \
  --outFileSortedRegions R1.bed

#Create a heatmap
plotHeatmap -m R1.gz \
-out 1.heatmap.png \
--regionsLabel "p1" "p2" \
--colorMap RdBu \
 --missingDataColor 0 \
 --heatmapHeight 15 \
--zMin 0 --zMax 4 \
--whatToShow 'heatmap and colorbar' \
--sortUsing max

[Marco Pannone]

Have you tried to tune also the parameter --heatmapWidth? I don't see it in your command line.

[minoo]

Yes but it just wider the heatmaps. It doesn't draw heatmaps next to each other horizontally.

[Marco Pannone]

Try plotting one heatmap at a time using the same --heatmapHeight and --heatmapWidth values.

[minoo]

Do you know how these arguments should be to give a single heatmap usually?

[Marco Pannone]

In order to plot one heatmap at a time you need to generate first two separate matrices per each .bed and .bw file, then input them to plotHeatmap.