DRviaSPCN (version 0.1.5)

Disease2SPheatmap: Plot a heat map of the subpathways activity regulated by disease

Description

The "Disease2SPheatmap" function plots a heat map of the subpathways that are regulated by disease. We map subpathways to the disease gene expression through ssgsea to get a subpathway abundance matrix. Then we visualize the matrix by heatmap.

Usage

Disease2SPheatmap(CentralityScore,ExpData,Label,pcut=0.05,bk=c(-2,2),
                  cluster.rows=FALSE,cluster.cols=FALSE,show.rownames=TRUE,
                  show.colnames=FALSE,col=c("navy","firebrick3"),
                  cell.width=NA,cell.height=NA,scale="row",fontsize=7,
                  fontsize.row=9,fontsize.col=10)

Value

A heat map

Arguments

CentralityScore

A dataframe with seven columns those are subpath ID, subpathway name, subpathway size, genes in subpathway, centralscore (eigenvector centrality), Pvalue and FDR.

ExpData

A gene expression profile of interest.

Label

A character vector consist of "0" and "1" which represent sample class in gene expression profile. "0" means normal sample and "1" means disease sample.

pcut

A numeric value which represent threshold. Subpathways with p-value less than this threshold will be screened out and visualized.

bk

A numeric vector that covers the range of values. Users could adjust color depth through this parameter.

cluster.rows

Boolean values determining if rows should be clustered or hclust object.

cluster.cols

Boolean values determining if columns should be clustered or hclust object.

show.rownames

Boolean specifying if row names are be shown.

show.colnames

Boolean specifying if column names are be shown.

col

Vector of colors used in heatmap.

cell.width

Individual cell width in points. If left as NA, then the values depend on the size of plotting window.

cell.height

Individual cell height in points. If left as NA, then the values depend on the size of plotting window.

scale

Character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none".

fontsize

Base fontsize for the plot (default: 10).

fontsize.row

Fontsize for rownames (default: 10).

fontsize.col

Fontsize for colnames (default: 10).

Examples

#Load depend package
library(GSVA)
library(pheatmap)
#Obtain input data (The "CentralityScoreResult" is the result of function "CalCentralityScore")
GEP<-GetExample('GEP')
Slabel<-GetExample('Slabel')
CentralityScoreResult<-GetExample('CentralityScoreResult')
#Run the function
#Disease2SPheatmap(CentralityScore=CentralityScoreResult,ExpData=GEP,Label=Slabel,
#                  pcut=0.05,bk=c(-2,2),cluster.rows=FALSE,cluster.cols=FALSE,
#                  show.rownames=TRUE,show.colnames=FALSE,col=c("navy","firebrick3"),
#                  cell.width=NA,cell.height=NA,scale="row",fontsize=7,
#                  fontsize.row=9,fontsize.col=10)