R/printGraph.R

In SubpathwayGMir: Identify Metabolic Subpathways Mediated by MicroRNAs

printGraph <-
function(ann,detail=FALSE){
	  if(detail==FALSE){
	  pathwayId<-sapply(ann,function(x) x$pathwayId)
      pathwayName<-sapply(ann,function(x) x$pathwayName)
      annMoleculeRatio<-sapply(ann,function(x) paste(x$annMoleculeNumber,x$moleculeNumber,sep="/"))
      annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
      pvalue<-sapply(ann,function(x) x$pvalue)
      fdr<-sapply(ann,function(x) x$fdr)
        ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annMoleculeRatio=annMoleculeRatio,
	  annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,stringsAsFactors=FALSE)							 
	  }
	  else{	 
      pathwayId<-sapply(ann,function(x) x$pathwayId)	  
	  pathwayName<-sapply(ann,function(x) x$pathwayName)
	  annMoleculeList<-sapply(ann, function(x){ paste(x$annMoleculeList,collapse=";") })
      annBgMoleculeList<-sapply(ann, function(x){ paste(x$annBgMoleculeList,collapse=";")})
	  annMoleculeRatio<-sapply(ann,function(x) paste(x$annMoleculeNumber,x$moleculeNumber,sep="/"))
      annBgRatio<-sapply(ann,function(x) paste(x$annBgNumber,x$bgNumber,sep="/"))
      pvalue<-sapply(ann,function(x) x$pvalue)
       fdr<-sapply(ann,function(x) x$fdr)
       ann.data.frame<-data.frame(pathwayId=pathwayId,pathwayName=pathwayName,annMoleculeRatio=annMoleculeRatio,
	  annBgRatio=annBgRatio,pvalue=pvalue,fdr=fdr,annMoleculeList=annMoleculeList,
	  annBgMoleculeList=annBgMoleculeList,stringsAsFactors=FALSE)								 
	  }
      return(ann.data.frame)
}