I want to use enhancedvolcanoes package to produce volcanoes plot, but the example is so confusing with its input data in 'S4' type, obj oriented. I have been looking for an example that shows simple data format that I need to have before inputing them in and use the package. Nowhere to be found!
I just have an excel sheet with 3 columns:
Gene, log2FoldChange, pvalue
When input into R as VC_data, can we seen as:
My code is as following:
EnhancedVolcano(VC_data, lab = VC_data$Gene, x = 'log2FoldChange', y = 'pvalue', xlim = c(-5, 8))
I keep getting this error saying that
'Error in EnhancedVolcano(VC_data, lab = VC_data$Gene, x = "log2FoldChange", : log2FoldChange is not numeric!'
When I did
is.numeric(VC_data$log2FoldChange), I get true.
I am very frustrated. Please help!