Change color of Diffbind's PCA and clustered heatmap plot()
3
0
Entering edit mode
melnuesch ▴ 10
@melnuesch-20883
Last seen 22 months ago

I changed the color palette from the dba.plotPCA very easily:

I defined

 mypalette=c()


(whatever colors I want) and then

 dba.plotPCA(results,DBA_CONDITION, label=DBA_ID,vColors=mypalette)


but I cannot seem to be able to do the same for the clustered heatmap (the one produced by plot(results) in DiffBind).

plot(results,vColors=mypalette)


or

plot(results,col=mypalette)


does not work. It says "error in plot.new() figure margins too large". I save it directly to a pdf file and does not complain, but when I open the picture has the default color palette all over again.

I also tried setting

palette(mypalette)


and then just running plot(results) but did not work, continued using the default one.

What can I do ? Because I want it to match the new colors I use in the PCA plot. Thank you for your time.

DiffBind plot color • 343 views
0
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 15 hours ago
CRUK, Cambridge, UK

plot() calls dba.plotHeatmap(), see the help page. You need to set the colScheme parameter to change the heatmap colors (using a colorRampPalette from RColorBrewer)

0
Entering edit mode
melnuesch ▴ 10
@melnuesch-20883
Last seen 22 months ago

But colScheme changes the color of the heatmap itself (the rectangles that in the default are green). I meant that I wanted to change the colors of the groups (Conditions) to match the color of the dots of the PCA plot. I want the heatmap to still be green but the condition groups to follow that other palette. I tried to change colScheme="Oranges", for example, but it did not do what I was looking for (just painted my heatmap rectangles orange). Do you have another solution? Thank you very much for your time.

0
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 15 hours ago
CRUK, Cambridge, UK

There are two parameters to dba.plotHeatmap() that control the colors of the attributes color bars: colSideCols and rowSideCols, are these the ones you want?

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