clusterHeatmap: Plots the cluster heatmap

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Plots the cluster heatmap

Description

Plots the cluster heatmap.

Usage

clusterResults(
  x,
  nClusters = 5,
  clusterColors = rainbow(nClusters),
  d = NULL,
  method = "ward.D2"
)

clusterHeatmap(
  x,
  param,
  result,
  file = "cluster-heatmap.png",
  method = "ward.D2",
  doClusterColumns = FALSE,
  columnDist = NULL,
  colColors = NULL,
  lim = c(-4, 4),
  lwid = c(1, 4),
  lhei = c(1, 5),
  cexRow = 1,
  cexCol = 1.5,
  labRow = rownames(x),
  margins = c(14, 9),
  colors = getBlueRedScale(),
  maxGenesWithLabel = 50,
  ...
)

goClusterResults(
  x,
  param,
  result,
  ontologies = c("BP", "MF", "CC"),
  seqAnno = NULL,
  universeGeneIds = NULL,
  universeProbeIds = NULL,
  keggOrganism = NA
)

Arguments

x	the data to plot.
method	a character representing the method to pass to hclust().
param	a list of parameters to extract the logical showGeneClusterLabels from.
result	a list of cluster result properties obtained with clusterResults().
file	a character representing the name of the .png file to derive tables from.
doClusterColumns	a logical indicating whether to do cluster columns.
columnDist	the distance matrix to use for the cluster columns.
colColors	used for the ColSideColors argument passed to heatmap.2().
lim	two integers used for breaks argument passed to heatmap.2().
cexRow	an integer passed to heatmap.2().
cexCol	an integer passed to heatmap.2().
labRow	a character vector, possibly modified, then passed to heatmap.2().
margins	an integer, possibly modified, then passed to heatmap.2().
colors	a character vector containing colors.
maxGenesWithLabel	an integer specifying the maximum amount of genes with labels.
...	additional arguments to be passed to heatmap.2().

Functions

• clusterResults(): Initializes and returns a list of results used by clusterHeatmap() and goClusterResults().

• goClusterResults(): Applies a GO analysis to the cluster results if GO should be done.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

hclust

heatmap.2

uzh/ezRun documentation built on March 5, 2025, 3:41 p.m.