heatmap_plot.rtf

{\rtf1\ansi\ansicpg1252\cocoartf1671\cocoasubrtf600
{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
{\*\expandedcolortbl;;}
\paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0
\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\pardirnatural\partightenfactor0

\f0\fs24 \cf0 \
### heatmap plot ###\
heatmap_plot <- function(m, groups, legend_colors, sample_names, type="normal", dendrogram="column", labrow="", bool_rowv=TRUE, bool_colv = TRUE, plot_path=NULL)\{\
\
  # load package\
  library(\'93gplots\'94)\
  \
  # create groups\
  names(colors) <- levels(groups)\
  \
  # replaces NAs with 0\
  m[is.na(m)] <- 0\
  colnames(m) <- sample_names\
  \
  # should rows be reordered\
  if (bool_rowv)\{\
    rowv <- as.dendrogram(hclust(dist(m)))\
  \} else \{\
    rowv <- FALSE\
  \}\
  \
  # should columns be reordered\
  if (is.logical(bool_colv))\{\
    if (bool_colv)\{\
      colv <- as.dendrogram(hclust(dist(t(m))))\
    \} else \{\
      colv <- FALSE\
    \}\
  \} else \{\
    colv <- bool_colv\
  \}\
  \
  # specify colors\
  if(is.null(legend_colors))\{\
    sidecolors <- rep("white", times=ncol(m))\
  \} else\{\
    sidecolors <- legend_colors[groups]\
  \}\
  \
  # create color palette\
  heatmap_pal <- colorRampPalette(rev(brewer.pal(11, "RdBu")))\
  \
  # plot heatmap\
  colors_pal <- colorRampPalette(pals::parula(40))\
  par(mfrow=c(1,1))\
  par(xpd=TRUE)\
  if (type == "normal")\{\
    heatmap.2(m,         \
              Rowv = rowv,\
              Colv=colv, \
              margins=c(8,8), cexCol = 1,labRow=labrow,col=heatmap_pal(50), ColSideColors = sidecolors, symkey = F,\
              cex.lab=1.5, scale="none", trace="none", dendrogram=dendrogram)\
  \}\
  if (type == "centered")\{\
    min_m <- min(m, na.rm=TRUE)\
    max_m <- max(m, na.rm=TRUE)\
    heatmap.2(m,         \
              Rowv = rowv,\
              Colv=colv,\
              labRow=labrow, margins=c(8,8), ColSideColors = sidecolors, trace="none",col=heatmap_pal(50),\
              breaks = seq(from=-2,to=2, length.out=51), \
              symkey = F,\
              dendrogram=dendrogram)\
    if(!is.null(plot_path))\{\
      pdf(file=plot_path, width = 6, height = 6)\
      heatmap.2(m,         \
                  Rowv = rowv,\
                  Colv=colv,\
                  labRow=labrow, margins=c(8,8), ColSideColors = sidecolors, trace="none",col=heatmap_pal(50),\
                  breaks = seq(from=-2,to=2, length.out=51), \
                  symkey = F,\
                  dendrogram=dendrogram)\
      dev.off()\
    \}\
  \} \
  if (type == "standardized")\{\
    min_m <- min(m, na.rm=TRUE)\
    max_m <- max(m, na.rm=TRUE)\
    heatmap.2(m,         \
              Rowv = rowv,\
              Colv= colv,\
              labRow=labrow, margins=c(8,8), ColSideColors = sidecolors, trace="none",col=heatmap_pal(50), symkey = F,\
              breaks = seq(from=-2,to=2, length.out=51),\
              dendrogram=dendrogram)\
    if (!is.null(plot_path))\{\
      pdf(file=plot_path, width = 6, height = 6)\
      heatmap.2(m,         \
                Rowv = rowv,\
                Colv= colv,\
                labRow=labrow, margins=c(8,8), ColSideColors = sidecolors, trace="none",col=heatmap_pal(50), symkey = F,\
                breaks = seq(from=-2,to=2, length.out=51),\
                dendrogram=dendrogram)\
      dev.off()\
    \}\
  \}\
  \
  # add legend\
  par(xpd=TRUE)\
\}}