cogena (version 1.6.2)

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

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.

...

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.v5.0.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)