heatmapPEI: 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)
"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)

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.

Value

a gene set enrichment heatmap

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)

Examples

Run this code

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)
# 
# #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)