[R] Enhanced Volcano plot

sudo apt install libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

BiocManager::install('EnhancedVolcano')

 

https://github.com/kevinblighe/EnhancedVolcano

 

 

dds <- DESeq(dds_1st, parallel = TRUE, betaPrior=FALSE)
res <- results(dds, alpha=1e-3)
res2  <- lfcShrink(dds, coef=2, type="apeglm", res=res) #, lfcThreshold=1)

volcanoes <- function(dataset, p, FC){
  keyvals <- rep('grey75', nrow(dataset))
  names(keyvals) <- rep('NS', nrow(dataset))
  
  keyvals[which(abs(dataset$log2FoldChange) > FC & dataset$pvalue > p)] <- 'forestgreen'
  names(keyvals)[which(abs(dataset$log2FoldChange) > FC & dataset$pvalue > p)] <- 'LFC'
  
  keyvals[which(abs(dataset$log2FoldChange) < FC & dataset$pvalue < p)] <- 'grey25'
  names(keyvals)[which(abs(dataset$log2FoldChange)  < FC & dataset$pvalue < p)] <- '-Log10Q'
  
  keyvals[which(dataset$log2FoldChange < -FC & dataset$pvalue < p)] <- 'blue2'
  names(keyvals)[which(dataset$log2FoldChange  < -FC & dataset$pvalue < p)] <- 'Down-regulated'
  
  keyvals[which(dataset$log2FoldChange > FC & dataset$pvalue < p)] <- 'red2'
  names(keyvals)[which(dataset$log2FoldChange > FC & dataset$pvalue < p)] <- 'Up-regulated'
  
  unique(keyvals)
  unique(names(keyvals))
  
  library(EnhancedVolcano)
  library(stringr)
  
  EnhancedVolcano(res2,
                  lab = rownames(dataset),
                  x = 'log2FoldChange',
                  y = 'pvalue',
                  #selectLab = rownames(dataset)[which(names(keyvals) %in% c('NS','log2FoldChange','-Log10Q','low','high'))],
                  xlim = c(-12,12),
                  xlab = bquote(~Log[2]~ 'fold change'),
                  ylab = bquote(~-Log[10] ~ italic(P)),
                  title = paste0('Volcano plot ( p > ', as.character(p), ' ,  LFC > ', as.character(FC),' )'),
                  titleLabSize = 16,
                  subtitle = paste0(' - Dataset : ',word(fname,-3, sep = '[/_]')),
                  pCutoff = p,
                  FCcutoff = FC,
                  pointSize = 1,
                  labSize = 3.5,
                  #shape = c(6, 4, 2, 11, 15),
                  colCustom = keyvals,
                  colAlpha = 0.7,
                  legendPosition = 'right',
                  legendLabSize = 12,
                  legendIconSize = 3.0,
                  drawConnectors = TRUE,
                  widthConnectors = 0.4,
                  axisLabSize = 13,
                  colConnectors = 'grey50',
                  gridlines.major = TRUE,
                  gridlines.minor = FALSE,
                  border = 'partial',
                  borderWidth = 0.6,
                  borderColour = 'black')
}

volcanoes(res, 1e-69, 1)

 

 

Reference

- lfcShrink: Shrink log2 fold changes, https://rdrr.io/bioc/DESeq2/man/lfcShrink.html