Plotting Upregulated and down regulated genes in different colour
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Somenath • 0
@c7ccb854
Last seen 2.7 years ago
United States

Hi, I wanted to plot up regulated genes in one color and down regulated genes in another color in enhanced volcano. I am totally naive, and I would appreciate if you let me know how to do it. I was using keyvals. colour, but probably I am writing it wrong.

up_path <- c(vj$logFC < -2.0)
down_path <- c(vj$logFC > 2.0)

## Print volcano plots with up genes in purple and down genes in green
keyvals.colour1 <- ifelse(
  rownames(vj) %in% up_path, 'purple',
  ifelse(rownames(vj) %in% down_path, 'green',
         'black'))

keyvals.colour1[is.na(keyvals.colour1)] <- 'black'
names(keyvals.colour1)[keyvals.colour1 == 'black'] <- 'NA'
names(keyvals.colour1)[keyvals.colour1 == 'purple'] <- 'vj$logFC < -2.0'
names(keyvals.colour1)[keyvals.colour1 == 'green'] <- 'vj$logFC > 2.0'


EnhancedVolcano(vj,
                lab = rownames(vj),
                x = 'logFC',
                y = 'pValue',
                selectLab = c('Axl','Mfge8','Gas6','Tyro3','S1pr1','Mertk'),
                xlim = c(-10, 10), 
                pCutoff = 0.001,
                FCcutoff = 1.5,
                boxedLabels = TRUE,
                drawConnectors = TRUE)
EnhancedVolcano • 1.2k views
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