pathwayHeatmap: Heatmap for pathways found by gene ontology analysis

In NBBttest: Negative Binomial Beta t-Test

Heatmap for pathways found by gene ontology analysis

Description

This function is used to show differential expressions of pathways or functions between conditions. These pathways or functions were detected by function annotation or gene ontology methods such as David function analysis tools or Ingenuity pathway analysis. Pathway score or pathway value is a weighted expression value across genes in a pathway or a function. The weigths of genes are given by p-values of enrichment or hit in function analysis.

Usage

pathwayHeatmap(dat, pathway, nci, r1, r2, colclass, rowclass, 
colrs, maptitle)

Arguments

dat	count dataset that contains a column for gene name and count data columns in two conditions.
pathway	a list that lists a function colomn and at least two gene columns. Row is function name.
nci	number of columns for gene information such as gene name, strand, chromosome, etc in dataset dat.
r1	number of replicates in condition 1 in dataset dat.
r2	number of replicates in condition 2 in dataset dat.
colclass	colonm class, equivalent to replicates in two conditions, such as c(1,1,1,1,2,2,2,2),meaning that condition A has 4 replicates and condition B has 4 replicates. Default =NULL.
rowclass	row class, pathway class, or pathway module. Default = NULL.
colrs	heatmap colors. User has 8 options: "redgreen", "greenred", "redblue", "bluered", "cm.colors", "terrain.colors","topo.colors", and"heat.colors".
maptitle	heatmap title, default = "".

Details

This function uses sigificance to choose gene function/ pathwaydata and then to normalize the selected data by using z-scale. This function has multiple options to select map color, distance, cluster and x- and y-lab angles.

Value

return a graph for heatmap.

Note

requres gplots and grDevices.

Author(s)

Yuan-De Tan [e-mail]

See Also

heatmap.2,myheatmap, myheatmap2

Examples

data(upGAm)
data(pathwy.A.up)
pathwayup<-pathwy.A.up
colclass=c("1","1","1","1","2","2","2","2","2","2")
oldpar <- par(no.readonly =TRUE)
on.exit(par(oldpar))
par(mar=c(7.5,5.5,3.5,3))
par(oma=c(3,1,1,10))
pathwayHeatmap(dat=upGAm,pathway=pathwayup,nci=1,
r1=4,r2=6,colclass=colclass,rowclass=NULL,
colrs="greenred",maptitle="pathway up-expression 
in Group A")

NBBttest documentation built on May 30, 2022, 1:05 a.m.