Hi everyone, 

This is the code I used to create a volcano plot: I am trying to plot several genes and highlight the top 20 most downregulated and top 20 most downregulated genes using green and red.

#Plot a volcano plot
  library(calibrate)
  head(afinal)
  threshold.high <- afinal$logFC[20]
  threshold.low <- sort(afinal$logFC, decreasing = FALSE)[20]
  file_nname <- sub('.csv','',file_name)
  plot_title = paste(file_nname, sep='-')
  with(afinal, plot(logFC, -log10(P.Value), pch=20, main = plot_title, xlim=c(-7,7)))
  with(subset(afinal, logFC>threshold.high), points(logFC, -log10(P.Value),pch=20, col='red'))
  with(subset(afinal, logFC<threshold.low),points(logFC, -log10(P.Value),pch=20, col="green"))
  with(subset(afinal,logFC>threshold.high | logFC<threshold.low), textxy(logFC, -log10(P.Value), labs=SYMBOL, cex= .8, offset = 0.8))

 However, I get overlapping gene labels. Is there anyway to avoid this? I know there is ggrepel but is there something similar for textxy?