Off topic:EnhancedVolcano - highlight specific points by changing colour.

Question

[n.tear]

Hi,

I am attempting to highlight a number of genes that intersect with a list of EMT genes I have.

When I run the below, any genes that are not EMT genes disappear.. How can I fix this?

top20padj <- head(res.smIHW.cp1df.rmNA.ord$symbol, n=20)
topLFCgenes <- res.smIHW.cp1df.rmNA.ord[order(-abs(res.smIHW.cp1df.rmNA.ord$shrunkLFC)), ]
top20LFCgenes <- head(topLFCgenes$symbol, n=20)

 # define genes that will show as shape 17
VolcanoEMTgenes <- as.vector(EMTgenes$`intersect(EMTdbgenes$GeneSymbol, res.smIHW.cp1df.rmNA.sig$symbol)`)

  # create custom key-value pairs for defined genes
  # this can be achieved with ifelse statements
  keyvals.shape <- ifelse(res.smIHW.cp1df.rmNA.ord$symbol %in% VolcanoEMTgenes, 17, 19)
  keyvals.shape[is.na(keyvals.shape)] <- 19
  names(keyvals.shape)[keyvals.shape == 17] <- 'EMT genes'


library(EnhancedVolcano)
EnhancedVolcano(res.smIHW.cp1df.rmNA.ord,
                lab = res.smIHW.cp1df.rmNA.ord$symbol,
                x = 'shrunkLFC',
                y = 'padj',
                title = '',
                subtitle = '',
                pCutoff = .05,
                FCcutoff = 2,
                pointSize = 3.0,
                labSize = 4.0,
                legendLabels=c('Not sig.','Log2 FC','p-value',
                               'p-value & Log2 FC'),
                selectLab = c(top20LFCgenes, top20padj),
               shapeCustom = keyvals.shape,
                drawConnectors = TRUE,
                widthConnectors = 0.2,
                colConnectors = 'grey30')