Drug2SPheatmap {DRviaSPCN}

Plot a heat map of the subpathways activity regulated by drugs

Description

The function "Drug2SPheatmap" plots heatmaps of the subpathways that are regulated by drugs. We map subpathways to the disease gene expression through ssgsea to get a subpathway abundance matrix. Then we visualize the matrix by heatmap.

Usage

Drug2SPheatmap(drugname="",DrugSPPvalue,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

drugname

A character which represent interest drug name with specific concentration, cell line and duration.

DrugSPPvalue

A matrix which colunms represent drugs and rows respresent subpathways. Values in this matrix is the pvalue of subpathways centrality score regulated by drugs.

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
#Statistic significance of centrality score of subpathways
#induced by each drug were stored in package "DRviaSPCNData".
#"DRviaSPCNData" has been uploaded to the github repository.
#Users can download and install through "install_github" function and
#set parameter url="hanjunwei-lab/DRviaSPCNData".
#After installing and loading package "DRviaSPCNData",
#users can use the following command to get the data:
#DrugSPPvalueMatrix<-GetData('DrugSPPvalueMatrix')
GEP<-GetExample('GEP')
Slabel<-GetExample('Slabel')

#Run the function
#Drug2SPheatmap(drugname = "methotrexate_HL60_6_8.8e-06",
#                 DrugSPPvalue=DrugSPPvalueMatrix,
#                 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)