Question Regarding PCA plot

[Miladebrahim]

Hi Igor,

Was wondering how can i set assign each group when running rna-star-groups-dge a specific color ?
I have only two groups and I would like to choose which is red and which is blue on the PCA
Thank you

[igordot]

The colors are defined in the deseq2-pca.R script. Specifically:

sns/scripts/deseq2-pca.R

Lines 47 to 55 in d59a37c

	# set color scheme based on the number of groups
	if (nlevels(fac) > 20) {
	colors = rainbow(nlevels(fac))
	} else if (nlevels(fac) > 2) {
	colors = unique(c(brewer.pal(5, "Set1"), brewer.pal(8, "Dark2"), brewer.pal(8, "Accent")))
	colors = colors[1:nlevels(fac)]
	} else {
	colors = c("dodgerblue3", "firebrick3")
	}

You can modify the script to fit your needs.