Is it possible to change color of nodes for cnetplot.compareClusterResult

[alexyfyf]

Hi Dr Yu,

Is it possible to change color of nodes for cnetplot.compareClusterResult and emapplot.compareClusterResult? By default the nodes are colored based on clusters, using ggplot color scheme. For example:

However, when one or more clusters don't have enriched terms, the color will automatically adjust. For example: In this case the color is different from the previous one, although in the same dataset. This inconsistency makes data interpretation difficult.

Is it possible to provide a fixed color for the clusters provided? Sorry if I missed it in you manual, but I really cannot get my head around it.

Thank you.

[lljotall]

Hello @alexyfyf,

I had the same question and found out that cnetplot returns a ggplot2 object, so we can use the same modifiers as we use for regular visualization. Check the example below based on the vignette example

library(org.Hs.eg.db)
library(clusterProfiler)

data(gcSample)
ck <- compareCluster(geneCluster = gcSample, fun = enrichKEGG)
ck <- setReadable(ck, OrgDb = org.Hs.eg.db, keyType="ENTREZID")
cnetplot(ck)
cnetplot(ck) + scale_fill_grey(start=0.8, end=0.2)
cnetplot(ck) + scale_fill_manual(values = rainbow(length(gcSample)))