R/Drug2SPheatmap.R

In DRviaSPCN: Drug Repurposing in Cancer via a Subpathway Crosstalk Network

##' @title 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.
##' @param drugname A character which represent interest drug name with specific concentration, cell line and duration.
##' @param 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.
##' @param ExpData A gene expression profile of interest.
##' @param 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.
##' @param pcut A numeric value which represent threshold. Subpathways with p-value less than this threshold will be screened out and visualized.
##' @param bk A numeric vector that covers the range of values. Users could adjust color depth through this parameter.
##' @param cluster.rows Boolean values determining if rows should be clustered or hclust object.
##' @param cluster.cols Boolean values determining if columns should be clustered or hclust object.
##' @param show.rownames Boolean specifying if row names are be shown.
##' @param show.colnames Boolean specifying if column names are be shown.
##' @param col Vector of colors used in heatmap.
##' @param cell.width Individual cell width in points. If left as NA, then the values depend on the size of plotting window.
##' @param cell.height Individual cell height in points. If left as NA, then the values depend on the size of plotting window.
##' @param 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".
##' @param fontsize Base fontsize for the plot (default: 10).
##' @param fontsize.row Fontsize for rownames (default: 10).
##' @param fontsize.col Fontsize for colnames (default: 10).
##' @return A heat map
##' @importFrom GSVA gsva
##' @importFrom GSVA ssgseaParam
##' @importFrom pheatmap pheatmap
##' @importFrom grDevices colorRampPalette
##' @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)
##' @export
##' @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)




Drug2SPheatmap<-function(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){
  haveGSVA <- PackageLoaded("GSVA")
  havepheatmap <- PackageLoaded("pheatmap")
  if (haveGSVA == FALSE) {
    stop("The 'GSVA' library, should be loaded first")
  }
  if (havepheatmap == FALSE) {
    stop("The 'pheatmap' library, should be loaded first")
  }

  sp<-GetExample('SubPathwayInfo')

  Drug_Pscore_matrix1 <- as.matrix(DrugSPPvalue[, which(colnames(DrugSPPvalue) ==  drugname)])
  colnames(Drug_Pscore_matrix1)<-drugname




  Drug_Pscore_matrix1<-names(which(Drug_Pscore_matrix1[,1]<pcut))

  sp<-sp[sp[,1]%in%Drug_Pscore_matrix1,]

  pl<-list()
  for (i in 1:length(sp[,1])) {
    pl[[i]]<-strsplit(sp[i,4],',')[[1]]
  }

  names(pl)<-sp[,1]

  #library(GSVA)
  ssgseaPar <- ssgseaParam(as.matrix(ExpData), pl,minSize=2)
  spw_matrix = gsva(ssgseaPar,verbose=T)

  colnames(spw_matrix)[which(Label=='0')]='normal'
  colnames(spw_matrix)[which(Label=='1')]='disease'
  spw_matrix<-spw_matrix[,order(colnames(spw_matrix))]
  colann=data.frame(Sample=factor(rep(names(table(colnames(spw_matrix))),
                                      table(colnames(spw_matrix)))))
  samples<-paste(colnames(spw_matrix),1:length(spw_matrix[1,]))
  colnames(spw_matrix)<-samples
  rownames(colann)<-samples
  colnames(colann)<-'Group'

  bk1<-c(seq(bk[1],-0.1,by=0.1),seq(0,bk[2],by=0.1))
  #library(pheatmap)
  heat.map<-pheatmap(spw_matrix,
                     scale = scale,
                     breaks = bk1,
                     color = colorRampPalette(c(col[1], "white", col[2]))(50),
                     cluster_rows=cluster.rows,cluster_cols=cluster.cols,
                     annotation_col =colann,
                     show_rownames=show.rownames,show_colnames=show.colnames,
                     cellwidth = cell.width,cellheight = cell.height,
                     fontsize = fontsize,fontsize_row = fontsize.row,
                     fontsize_col = fontsize.col,
                     main = paste("Heatmap of the activities of significant subpathways regulated by the",
                                  drugname)

  )
}