R/plotHeatmap.R

In jhsiao999/Humanzee: Tools for statistical analysis of genomics data

#' Plot a heatmap of GO terms
#'
#' @param heatmapData matrix generated by Humanzee::goHeatmapData, which contains
#'                    GO terms annotations and p-values of the enrichment analysis.
#'
#' @return hmp heatmap generated by heatmap.2 function.
#'
#' @export
#'
#' @examples
#'  hmap <- plotHeatmap(heatmap_allgos,
#'                      labCol = c("Ribo > mRNA", "RNA > Ribo",
#'                                "Ribo > Protein", "Protein > Ribo"))
plotHeatmap <- function(heatmapData, mar =  c(0, 0, 0, 0),
                        oma = c(0, 0, 0, 0), keysize = .5,
                        labCol = "" ) {
  require(broman)
  crayon <- brocolors("crayon")
  cols =  colorRampPalette(c("white", crayon["Banana Mania"],
                             crayon["Laser Lemon"],
                             crayon["Burnt Orange"], crayon["Orange Red"],
                             crayon["Plum"]))
  par( mfrow = c(1,1), mar = mar, oma = oma )
  require(gplots)
  mat <- matrix(heatmapData[ , -c(1:2)], ncol = 1)
  sepwidth <- c(.1, .01)
  sepcol <- "grey30"

  if (NCOL(mat) == 1) {
    mat <- cbind(mat, mat)
    sepwidth <- c(0, .01)
    sepcol <- "white"
  }
  rownames(mat) <- heatmapData$Term
  hmap <- heatmap.2(as.matrix(-log10(mat)), main = "",
                    labCol = labCol, cexCol = 1.2,
                    cexRow = 1.3,
                    sepcol = "white", sepwidth=sepwidth,
                    colsep = 1:ncol(mat), Colv = FALSE,
                    rowsep = 1:nrow(mat), dendrogram = "row",
                    srtCol = 0, adjCol = c(.5,NA), offsetCol = 1,
                    keysize = keysize, lwid = c(1.5, 7), lhei = c(.5, 5),
                    col = cols, trace ="none", key.title = "-log p-value" )
  return(hmap)
}