Hello, I am trying to make a volcano plot for different clusters. I have 2 conditions, untreated vs. treated. I have a differential expression excel file that cellranger generated for me but within the file it has multiple clusters each which have a fold change and p value. How do I create a volcano plot that contains all the clusters rather than one? Would I have to do a volcano plot for each cluster and then combine them all somehow?
I use this code to generate the plot for just one of the clusters...
macrophage_list <- read.table("differential_expression_macrophage.csv", header = T, sep = ",") EnhancedVolcano(macrophage_list, lab = as.character(macrophage_list$FeatureName), x = 'untreated.Log2.Fold.Change', y = 'untreated.P.Value', xlim = c(-8,8), title = 'Macrophage', pCutoff = 10e-5, FCcutoff = 1.5, pointSize = 3.0, labSize = 3.0)
Any help and suggestions is greatly appreciated.