heatmapCmap: heatmap designed for for CMap gene set only

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

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,
  geom = "tile"
)

## S4 method for signature 'cogena'
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,
  geom = "tile"
)

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.
geom	tile or circle

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

Value

a gene set enrichment heatmap

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)

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