R/GSEA.HeatMapPlot2.R

In RaikOtto/GeneraPipe:

GSEA.HeatMapPlot2 <- function(V, row.names = "NA", col.names = "NA", main = " ", sub = " ", xlab=" ", ylab=" ", color.map = "default") {
  #
  # Plots a heatmap of a matrix
  
  n.rows <- length(V[,1])
  n.cols <- length(V[1,])
  
  if (color.map == "default") {
    color.map <- rev(rainbow(100, s = 1.0, v = 0.75, start = 0.0, end = 0.75, gamma = 1.5))
  }
  
  heatm <- matrix(0, nrow = n.rows, ncol = n.cols)
  heatm[1:n.rows,] <- V[seq(n.rows, 1, -1),]
  
  par(mar = c(7, 15, 5, 5))
  image(1:n.cols, 1:n.rows, t(heatm), col=color.map, axes=FALSE, main=main, sub = sub, xlab= xlab, ylab=ylab)
  
  if (length(row.names) > 1) {
    size.row.char <- ifelse(n.rows < 15, 1, sqrt(15/n.rows))
    size.col.char <- ifelse(n.cols < 15, 1, sqrt(10/n.cols))
    #            size.col.char <- ifelse(n.cols < 2.5, 1, sqrt(2.5/n.cols))
    for (i in 1:n.rows) {
      row.names[i] <- substr(row.names[i], 1, 40)
    }
    row.names <- row.names[seq(n.rows, 1, -1)]
    axis(2, at=1:n.rows, labels=row.names, adj= 0.5, tick=FALSE, las = 1, cex.axis=size.row.char, font.axis=1, line=-1)
  }
  
  if (length(col.names) > 1) {
    axis(1, at=1:n.cols, labels=col.names, tick=FALSE, las = 3, cex.axis=size.col.char, font.axis=2, line=-1)
  }
  
  return()
}