complexHeatmap-methods: description of function plot.beans
In stela2502/StefansExpressionSet: StefansExpressionSet

complexHeatmap

R Documentation

description of function plot.beans

Description

plot the PCR heatmap using the heatmap.3 function included in this package

Usage

complexHeatmap(x, ofile = NULL, colGroups = NULL, rowGroups = NULL,
  colColors = NULL, rowColors = NULL, pdf = FALSE, subpath = "",
  main = "", heapmapCols = function(x) {     c("darkgrey", bluered(x)) },
  brks = 10, X11type = "cairo")

Arguments

`x`	the StefansExpressionSet object
`ofile`	the outfile to create in the x@outpath folder
`colGroups`	columns in the samples table to use to order the data (first == order)
`rowGroups`	rows in the annotation table to use to color the heatmap rows (first == order)
`colColors`	a named list of column color vectors
`rowColors`	a named list of row color vectors
`pdf`	export as pdf (default = FALSE)
`subpath`	the subpath for the plots (default = ”)
`heapmapCols`	the color function to calculate the heatmap colours ( default function (x) c("darkgrey",bluered(x)) )
`brks`	how many breaks should the expression value color key have (default=10)