Disease2SPheatmap {DRviaSPCN} | R Documentation |
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)
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). |
Value
A heat map
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)