complexHeatmap-methods: description of function complexHeatmap

Description Usage Arguments

Description

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

Usage

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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. 23, 2022, 5:47 a.m.