rggplot2ggpubr

Is it possible to only label the genes that are only positive or up regulated ones?

ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
         fdr = 0.05, fc = 2, size = 0.4, 
         genenames = as.vector(diff_express$name),
         ggtheme = ggplot2::theme_minimal(),
         top = 0, label.select = c("BUB1", "CD83")
         )

The figure that is generated this.

I want only to put labels which are unregulated or red marked not the down ones. One way to achieve is I can do this only for up regulated genes by using this

label.select = c("BUB1", "CD83")

But instead of doing this where I have to add label manually can do it other way or methods

Any suggestion or help would be really appreciated

enter image description here

Solution

  • The question is about subsetting the data, see below example and adapt as needed:

    # log2FoldChange more than 5
myGenes <- diff_express[ diff_express$log2FoldChange > 5, ]
# rank them by Pvalue, get top 5
myGenes <- myGenes[ rank(myGenes$padj) <= 5, "name"]
# some genes do not have a name, exclude
myGenes <- myGenes[ !is.na(myGenes) & myGenes != ""]

ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"),
         fdr = 0.05, fc = 2, size = 0.4, 
         genenames = as.vector(diff_express$name),
         ggtheme = ggplot2::theme_minimal(),
         top = 0, label.select = myGenes)

    enter image description here