color specific genes in VariableFeaturePlot

Question

[Assa Yeroslaviz]

I was wondering if it is possible to color specific genes in a VariableFeaturePlot from the Seurat package.

I have a vector of names i use to label them, but I would like to also add a different color to a second vector of genes.

This how I label them for now:

plot1 <-  VariableFeaturePlot(C7_G7) +
  scale_color_manual(values = c("purple", "lightblue", "red")) 

genes <- c("Gzma", "Ighg1", head(VariableFeatures(C7_G7), 10))
plot2 <- LabelPoints(plot = plot1, points = genes, repel = TRUE, 
                     max.overlaps = Inf, xnudge = 0, ynudge = 0)

But how can I color specific points in the plot?

thanks

Answer 1

[Bastien Hervé]

plot1 <-  VariableFeaturePlot(C7_G7)

genes_colors <- c("Gzma"="orange", "Ighg1"="red") #Add more genes and colors
plot1$data[names(genes_colors),]$colors <- names(genes_colors) #Replace the no/yes with your gene names

plot2 <- plot1 + scale_color_manual(values=c("no"="purple", "yes"="lightblue", genes_colors))

plot3 <- LabelPoints(plot = plot2, points = names(genes_colors), repel = TRUE, max.overlaps = Inf, xnudge = 0, ynudge = 0)