I am working on the MA plot.
I would like,
1) To color the upregulated genes with red
2) To color the downregulated genes with blue
3) Add labels to some of the genes
I tried one of the package ggpur (ggmaplot),
maplot = ggmaplot(contrast_results, fdr = 0.05, fc = 1, size = 1,palette = c("#B31B21", "#1465AC", "darkgray"),genenames = as.vector(contrast_results$name),legend="top", top = 15,font.label = c("bold", 10),label.rectangle = TRUE, font.legend = c("bold",12),font.main = "bold")
In general the resolution is bad and the dots are too small and even the legend for the color is too small.
Anybody worked on this package before or any other suggestions are welcomed to accomplish the above three things.