complexHeatmap-methods: description of function complexHeatmap

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

description of function complexHeatmap

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", gplots::bluered(x)) },
  brks = 10,
  X11type = "cairo",
  green = F,
  noBreaks = F,
  family = "Helvetica"
)

Arguments

x	the BioData 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 = ”)
main	the picture title (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)
X11type	sometimes needed for compatibility (default = 'cairo')
green	if in SingleCell mode normalization losses get a -1 and can be displayed as green or black in the default coloring (default green=F => black)
noBreaks	show linear data colors instead of bined ones; impossible if green=TRUE (default =FALSE)
family	the grDevices font family (default 'Helvetica')

stela2502/BioData documentation built on Feb. 27, 2025, 6:20 a.m.