heatmapPEI: heatmap of the gene set enrichment from a cogena object.

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

heatmap of the gene set enrichment from a cogena object.

Description

heatmap of the gene set enrichment score. After obtaining the ennrichemt of clusters for each gene set, the heatmapPEI will show it as a heatmap in order. The value shown in heatmapPEI is the -log2(fdr), representing the enrichment score.

Usage

heatmapPEI(
  object,
  method,
  nCluster,
  CutoffNumGeneset = 20,
  CutoffPVal = 0.05,
  orderMethod = "max",
  roundvalue = TRUE,
  low = "grey",
  high = "red",
  na.value = "white",
  maintitle = NULL,
  printGS = FALSE,
  add2 = TRUE,
  geom = "tile",
  wrap_with = 40
)

## S4 method for signature 'cogena'
heatmapPEI(
  object,
  method = clusterMethods(object),
  nCluster = nClusters(object),
  CutoffNumGeneset = 20,
  CutoffPVal = 0.05,
  orderMethod = "max",
  roundvalue = TRUE,
  low = "grey",
  high = "red",
  na.value = "white",
  maintitle = NULL,
  printGS = FALSE,
  add2 = TRUE,
  geom = "tile",
  wrap_with = 60
)

Arguments

object	a genecl or cogena object
method	as clMethods in genecl function
nCluster	as nClust in cogena function.
CutoffNumGeneset	the cut-off of the number of gene sets in the return table
CutoffPVal	the cut-off of p-value. The default is 0.05.
orderMethod	the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.
roundvalue	The default is TRUE. whether or not round the data. such as round(1.54, 1)=1.5
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. like GSExxx. the output of figure will like "cogena: kmeans 3 GSExxx" in two lines. 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
wrap_with	default 40. wrap strings

Details

The x-axis shows cluster i and the number of genes in cluster, with red means cluster containing up-regulated genes, green means down-regulated genes, black means there are up and down regulated genes in this cluster and blue means all DEGs. If parameter add2 is true, another two columns will be shown as well, representing the up and down regulated genes.

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.

The y-axis represents the gene sets enriched.

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)

Value

a gene set enrichment heatmap

See Also

clEnrich and heatmapCluster

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)

#heatmapPEI
heatmapPEI(clen_res, "kmeans", "2")
heatmapPEI(clen_res, "kmeans", "2", orderMethod="mean")
heatmapPEI(clen_res, "kmeans", "3", CutoffNumGeneset=20, 
    low = "#132B43", high = "#56B1F7", na.value = "grey50")

## End(Not run)

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