Hi Igor, Was wondering how can i set assign each group when running

The colors are defined in the deseq2-pca.R . Sp

Question Regarding PCA plot about sns HOT 1 CLOSED

Miladebrahim commented on May 26, 2024

Question Regarding PCA plot

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Comments (1)

igordot commented on May 26, 2024

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.

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	# 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")
	}