cogena (version 1.6.2)

heatmapCmap: heatmap designed for for CMap gene set only

Description

heatmapCmap is desgined for the cogena result from CMap only so as to collapse the multi-isntance drugs in CMap!

Usage

heatmapCmap(object, method = clusterMethods(object), nCluster = nClusters(object), orderMethod = "max", MultiInstance = "drug", CutoffNumGeneset = 20, CutoffPVal = 0.05, mergeMethod = "mean", low = "grey", high = "red", na.value = "white", maintitle = NULL, printGS = FALSE, add2 = TRUE)
"heatmapCmap"(object, method = clusterMethods(object), nCluster = nClusters(object), orderMethod = "max", MultiInstance = "drug", CutoffNumGeneset = 20, CutoffPVal = 0.05, mergeMethod = "mean", low = "grey", high = "red", na.value = "white", maintitle = "cogena", printGS = FALSE, add2 = TRUE)

Arguments

object

a genecl or cogena object

method

as clMethods in genecl function

nCluster

as nClust in cogena function.

orderMethod

the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.

MultiInstance

merge multi instances. Options are "drug", "celldrug", "conccelldrug", "concdrug".

CutoffNumGeneset

the cut-off of the number of gene sets in the return table. The default is 20.

CutoffPVal

the cut-off of p-value. The default is 0.05.

mergeMethod

max or mean. The default is mean.

low

colour for low end of gradient.

high

colour for high end of gradient.

na.value

Colour to use for missing values.

maintitle

a character. Default is null

printGS

print the enriched gene set names or not. Default is FALSE

add2

enrichment score for add Up and Down reuglated genes.

Value

a gene set enrichment heatmap

Details

orderMethod:

• max. ordered by the max value in clusters beside all
• mean. ordered by the mean value in clusters beside all
• All. ordered by all genes
• Up. ordered by up-regulated genes (add2 should be TRUE)
• Down. ordered by down-regulated genes (add2 should be TRUE)

MultiInstance:

• drug. merge based on cmap_name
• celldrug. merge based on cmap_name and cell type
• conccelldrug. merge based on cmap_name, cell type and concentration

Examples

data(Psoriasis)
annofile <- system.file("extdata", "CmapDn100.gmt.xz", package="cogena")
## Not run: 
# genecl_result <- coExp(DEexprs, nClust=3, clMethods=c("pam"), 
#     metric="correlation", method="complete", ncore=2, verbose=TRUE)
# clen_res1 <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)
# 
# heatmapCmap(clen_res1, "pam", "3", orderMethod="2")
# heatmapCmap(clen_res1, "pam", "3", orderMethod="2", MultiInstance="concdrug")
# ## End(Not run)