How can I set `plotheatmap` to different colors for different `.bed` file regions?

[danli349]

How can I set plotheatmap to different colors for different .bed file regions?

I want to set the up panel as 'white,red' and the lower panel as 'white,blue'.

and how can I change the color of the intensity curve to red and blue?

Thanks

[dpryan79]

Give multiple values to --colorList, such as --colorList “white,red” “white,blue”. Note the space between the values for separate heatmaps. The same concept applies to plotProfile --colors option.

[danli349]

@dpryan79
I tried --colorList “white,red” “white,blue”,
But it will change the color of different samples, not different regions.

[dpryan79]

Ah, yeah we don't support per-region heat maps. You might want to plot them separately and then merge the images into the same figure.

[danli349]

@dpryan79
How can I change the color of the intensity curve?

[dpryan79]

--colors. That plot has multiple samples merged together I believe.

[danli349]

@dpryan79

I tried --colors parameter:

plotHeatmap  -m plotHeatmap/matrix.gz \
-out plotHeatmap/plotHeatmap_ET.pdf \
--outFileSortedRegions plotHeatmap/HisMod_2K_Out_ET.bed \
--regionsLabel "ET_up" "ET_down" \
--missingDataColor white \
--dpi 500 \
--samplesLabel "EY" "ET" \
--colors "red" "blue" \
--colorList 'white,red' 'white,blue' \
--yMin 0 \
--zMin 0

But I got error:
plotHeatmap: error: unrecognized arguments: --colors red blue
There is no --colors arguments in plotHeatmap.

[dpryan79]

Sorry, I thought you were directly using plotProfile. Since the heatmap is kind of the star of the show in plotHeatmap there's no option to change the profile color.

[niekwit]

I have created a PR that allows to set the colours for the profile plot: #1427.