Hi All,

How can I specify the color that I would like to use in plotMutationSpectrum()?

eg.

plotMutationSpectrum(sca_motifs, "study", normalize = TRUE), I would like to only use "red" color here, 

or plotMutationSpectrum(sca_motifs, "study",colorby = c("alteration"), normalize = TRUE), if I would like to multiple colors. 

how should I do?

Thanks,

Rebecca

For the first case with only one color for all studies/samples, use the following:

p = plotMutationSpectrum(sca_motifs, "study", normalize = TRUE)
p = p + scale_fill_manual(values = rep("darkred", nlevels(p$data$sample))) ## uses "darkred" as color
p

For your second case, can you specific what you mean with "multiple colors"? The plot already uses different colors to distinguish the mutational motifs.