Dear all here, just wondering how to color specific node or gene symbol from cnetplot?

library(DOSE)
library(enrichplot)
library(clusterProfiler)
data(geneList)
deg <- names(geneList)[abs(geneList) > 2]
enrichment.result <- enrichDGN(deg)
edox <- setReadable(enrichment.result, "org.Hs.eg.db", "ENTREZID")
cnt_enrichment <- enrichplot::cnetplot(edox)

Now in the plot I would like to color the node or the gene symbol itself of the following MARCO, GZMB, CXCL11, CXCL10 LAG3, CCL8 as red and PDK1, GABRP, MELK and CENPE as blue.

I would appreciate it if someone could show me how to do it. Thanks ADR

I think you should be able to specify that with the 'color_gene' argument, but I can't figure out how one might do that. Failing to accomplish it that way, there is always the 'hack at it until you get what you want'.

## extract the data object from the ggplot object
dat <- cnt_enrichment$data
## change the colors
dat$color[dat$name %in% c("MARCO", "GZMB", "CXCL11", "CXCL10", "LAG3", "CCL8")] <- "#FF0000"
dat$color[dat$name %in% c("PDK1", "GABRP", "MELK", "CENPE")] <- "#0000FF"
## stuff it back in there
cnt_enrichment$data <- dat
## check it out
cnt_enrichment

Here is the answer:

foldChange = c(rep(1, 6), rep(-1, 4))
names(foldChange) <- c("MARCO", "GZMB", "CXCL11", "CXCL10", 
                "LAG3", "CCL8", "PDK1", "GABRP", "MELK", "CENPE")
p <- cnetplot(edox, foldChange=foldChange)

1. you may want to disable the legend, then:

p <- cnetplot(edox, foldChange=foldChange) + guides(color='none')

1. you may want to add a legend for the color you specify:

d = data.frame(type=c('upregulated', 'downregulated'), x=0, y=0)
p + geom_point(aes(alpha=type, x=x, y=y), data=d, shape=16, size=0)  + 
    guides(alpha=guide_legend(
                    override.aes=list(color=c("blue", "red"), 
                                    alpha=1, 
                                    size=3)
                            )
            )