heatmapCluster: heatmap of gene expression profilings with cluster...

In zhilongjia/cogena: co-expressed gene-set enrichment analysis

heatmap of gene expression profilings with cluster indication.

Description

heatmap of gene expression profilings with cluster-based color indication. The direction of DEGs are based on latter Vs former from sample labels. For example, labels are as.factor(c("ct", "Disease")), the "Disease" are latter compared with "ct". Usually, the order is the alphabet.

Usage

heatmapCluster(
  object,
  method,
  nCluster,
  scale = "row",
  sampleColor = NULL,
  clusterColor = NULL,
  clusterColor2 = NULL,
  heatmapcol = NULL,
  maintitle = NULL,
  printSum = TRUE,
  add2 = TRUE,
  cexCol = NULL,
  ...
)

## S4 method for signature 'cogena'
heatmapCluster(
  object,
  method = clusterMethods(object),
  nCluster = nClusters(object),
  scale = "row",
  sampleColor = NULL,
  clusterColor = NULL,
  clusterColor2 = NULL,
  heatmapcol = NULL,
  maintitle = NULL,
  printSum = TRUE,
  add2 = TRUE,
  cexCol = NULL,
  ...
)

Arguments

object	a genecl or cogena object
method	as clMethods in genecl function
nCluster	as nClust in cogena function.
scale	character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is "row".
sampleColor	a color vector with the sample length. The default is from topo.colors randomly.
clusterColor	a color vector with the cluster length. The default is rainbow(nClusters(object)).
clusterColor2	a color vector with 2 elements. The default is rainbow(2).
heatmapcol	col for heatmap. The default is greenred(75).
maintitle	a character. like GSExxx. the output of figure will like "kmeans 3 Clusters GSExxx" in two lines.
printSum	print the summary of the number of genes in each cluster. Default is TRUE.
add2	add 2 clusters information.
cexCol	numbers, used as cex.axis in for the column axis labeling.
...	other parameters to heatmap.3.

Value

a gene expression heatmap with Cluster information figure

See Also

clEnrich, heatmap.3 and heatmapPEI

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", 
package="cogena")

## Not run: 
genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), 
    metric="correlation", method="complete", ncore=2, verbose=TRUE)

clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

#summay this cogena object
summary(clen_res)

#heatmapCluster

heatmapCluster(clen_res, "hierarchical", "3")
heatmapcol <- gplots::redgreen(75)
heatmapCluster(clen_res, "hierarchical", "3", heatmapcol=heatmapcol)

## End(Not run)

zhilongjia/cogena documentation built on Nov. 21, 2023, 1:34 a.m.