R/GE.R

In guokai8/EnrichR: Functional Enrichment analysis

#' GO Enrichment analysis function
#' @importFrom dplyr filter_
#' @param df DGE files (DESeq2 result files) or vector contains gene names
#' @param GO_FILE GO annotation data
#' @param OP use BP,CC or MF
#' @param minSize minimal number of genes included in significant terms
#' @param padj.method p value adjust method (default: BH)
#' @param cutoff cutoff value for filtering significant terms (default: 0.05)
#' @param maxSize maximum number of genes included in significant terms
#' @param keepRich keep terms with rich factor value equal 1 or not (default: TRUE)
#' @param filename output filename
#' @param gene.cutoff the cut-off value for select DEGs (default: 0.01)
#' @export
#' @author Kai Guo
GE<-function(df,GO_FILE,OP="BP",gene.cutoff=0.01,minSize=2,maxSize=500,keepRich=TRUE,filename=NULL,padj.method="BH",cutoff=0.05){
  go2gene<-sf(GO_FILE)
  all_go<-.get_go_dat(ont = OP)
  go2gene<-go2gene[names(go2gene)%in%rownames(all_go)];
  gene2go<-reverseList(go2gene)
  if(is.data.frame(df)){
    IGE<-rownames(df)[df$padj<gene.cutoff]
  }else{
    IGE=as.vector(df)
  }
  fgene2go<-gene2go[IGE];
  fgo2gene<-reverseList(fgene2go)
  k=name_table(fgo2gene);
  n=sum(!is.na(names(fgene2go)))
  IGO<-names(fgo2gene);
  N=length(unique(unlist(go2gene)));
  M<-name_table(go2gene[IGO])
  rhs<-hyper_bench_vector(k,M,N,n)
  lhs<-p.adjust(rhs,method=padj.method)
  rhs_an<-all_go[names(rhs),]
  rhs_gene<-unlist(lapply(fgo2gene, function(x)paste(unique(x),sep="",collapse = ",")))
  resultFis<-data.frame("Annot"=names(rhs),"Term"=rhs_an,"Annotated"=M[names(rhs)],
                        "Significant"=k[names(rhs)],"Pvalue"=as.vector(rhs),"Padj"=lhs,
                        "GeneID"=rhs_gene[as.vector(names(rhs))])
  resultFis<-resultFis[order(resultFis$Pvalue),]
  resultFis<-resultFis[resultFis$Pvalue<cutoff,]
  resultFis<-filter_(resultFis, ~Significant<=maxSize)
  if(keepRich==FALSE){
    resultFis<-filter_(resultFis, ~Significant>=minSize)
  }else{
    resultFis<-filter_(resultFis, ~Significant>=minSize|(~Annotated/~Significant)==1)
  }
  if(!is.null(filename)){
    write.table(resultFis,file=paste(filename,OP,"res.txt",sep="_"),sep="\t",quote=F,row.names=F)
  }
  return(resultFis);
}
#' Display GO enrichment result
#' @param resultFis: GO ennrichment analysis result data.frame
#' @param top: Number of Terms you want to display
#' @param filename: output filename
#' @param pvalue.cutoff: the cut-off value for selecting Term
#' @param padj.cutoff: the padj cut-off value for selecting Term
#' @param usePadj use adjust pvalue or not
#' @param low color used for small value
#' @param high color used for large value
#' @param order order bar or not
#' @param horiz use horiz or not
#' @param fontsize.x fontsize for x axis
#' @param fontsize.y fontsize for y axis
#' @param filename output filename
#' @param width width for output file
#' @param height height for output file
#' @param angle angle for x ticks label
#' @param horiz horizontal plot or not (default: FALSE)
#' @export
#' @author Kai Guo
GE.plot<-function(resultFis,top=50,pvalue.cutoff=0.05,order=FALSE,horiz=FALSE,
                  low="lightpink",high="red",
                  font.x="bold",font.y="bold",fontsize.x=10,fontsize.y=10,
                  fontsize.text=3,angle=75,padj.cutoff=NULL,usePadj=TRUE,
                  filename=NULL,width=10,height=8){
    require(ggplot2)
    if(!is.null(padj.cutoff)){
      resultFis<-resultFis[resultFis$Padj<padj.cutoff,]
    }else{
      resultFis<-resultFis[resultFis$Pvalue<pvalue.cutoff,]
    }
    if(nrow(resultFis)>=top){
      resultFis<-resultFis[1:top,]
    }
    if(max(resultFis$Significant/(resultFis$Annotated+0.1))<=1){
      yheight=max(resultFis$Significant/resultFis$Annotated)+0.1
    }else{
      yheight=1
    }
    if(order==TRUE){
      resultFis$rich<-as.numeric(resultFis$Significant)/as.numeric(resultFis$Annotated)
      resultFis$Term<-factor(resultFis$Term,levels=resultFis$Term[order(resultFis$rich)])
    }
    if(usePadj==FALSE){
      p<-ggplot(resultFis,aes(x=Term,y=round(as.numeric(Significant/Annotated),2)))+geom_bar(stat="identity",aes(fill=-log10(as.numeric(Pvalue))))
      p<-p+scale_fill_gradient(low=low,high=high)+theme_light()
      if(horiz==TRUE){
        p<-p+theme(axis.text.y=element_text(face=font.y,size=fontsize.y),axis.text.x=element_text(face=font.x,color="black",size=fontsize.x,angle=angle))+labs(fill="-log10(Pvalue)")
        p<-p+coord_flip()
        p<-p+geom_text(aes(label=Significant),hjust=-0.3,size=fontsize.text)+xlab("Annotation")+ylab("Rich Factor")+ylim(0,yheight)
       }else{
         p<-p+theme(axis.text.y=element_text(face=font.y,size=fontsize.y),axis.text.x=element_text(face=font.x,color="black",size=fontsize.x,angle=angle,vjust=1,hjust=1))+labs(fill="-log10(Pvalue)")
         p<-p+geom_text(aes(label=Significant),vjust=-0.3,size=fontsize.text)+xlab("Annotation")+ylab("Rich Factor")+ylim(0,yheight)
      }
      print(p)
    }else{
    p<-ggplot(resultFis,aes(x=Term,y=round(as.numeric(Significant/Annotated),2)))+geom_bar(stat="identity",aes(fill=-log10(as.numeric(Padj))))
    p<-p+scale_fill_gradient2(low=low,high=high)+theme_light()
      if(horiz==TRUE){
      p<-p+theme(axis.text.y=element_text(face=font.y,size=fontsize.y),axis.text.x=element_text(face=font.x,color="black",size=fontsize.x,angle=angle))+labs(fill="-log10(Padj)")
      p<-p+coord_flip()
      p<-p+geom_text(aes(label=Significant),hjust=-0.3,size=fontsize.text)+xlab("Annotation")+ylab("Rich Factor")+ylim(0,yheight)

    }else{
      p<-p+theme(axis.text.y=element_text(face=font.y,size=fontsize.y),axis.text.x=element_text(face=font.x,color="black",size=fontsize.x,angle=angle,vjust=1,hjust=1))+labs(fill="-log10(Padj)")
      p<-p+geom_text(aes(label=Significant),vjust=-0.3,size=fontsize.text)+xlab("Annotation")+ylab("Rich Factor")+ylim(0,yheight)
    }
        print(p)
    }
    if(!is.null(filename)){
      ggsave(p,file=paste(filename,OP,"enrich.pdf",sep="_"),width=width,height=height)
    }
}