This script is to read a CSV file that contain a list of genes in HGNC format in each column and will plot the GO enrichment analysis using DAVID webservice.

gistfile1.r

 DoDAVIDGOAnnotation <-function(topics,pval=0.05,GOlimit=5){
    
    clusters<-1:ncol(topics)
    
    Groups<-c();
    Annot<-c();
    pvalue<-c();
    counts<-c();
    for(clus in clusters){
        #Get the genes in that cluster
        inCluster<-as.character(topics[,clus]);
        inCluster<-inCluster[inCluster!=""];
        
        #Get GO enrichment from DAVID
        dav<-DAVIDQuery(ids=inCluster,type="OFFICIAL_GENE_SYMBOL",annot="GOTERM_BP_ALL",tool="chartReport",URLlengthLimit = 102400);
        
        if(length(dav$downloadFileName)>0){
            dav$DAVIDQueryResult$Benjamini<-as.double(dav$DAVIDQueryResult$Benjamini);
            sigGO<-subset(dav$DAVIDQueryResult[-1,], Benjamini <= pval);
            
            #if we have some significant annotation
            if(nrow(sigGO)>0){
                if(nrow(sigGO)>GOlimit ) {sigGO<-sigGO[1:GOlimit,] }
                #anot<-as.character( paste( sigGO$Term, "(" , sigGO$Count, ")", sep="") )
                #Annot<-c(Annot,anot)                           
                Annot<-c(Annot,sigGO$Term)
                sigGO$Count<-as.integer(sigGO$Count)
                counts<-c(counts,sigGO$Count/length(inCluster))
                gr<-paste(clus,"(",length(inCluster),")",sep="")
                Groups<-c(Groups,rep(gr,length(sigGO$Term)));
                pvalue<-c(pvalue,sigGO$Benjamini);
            }           
        }
        Sys.sleep(10)
    }
    
    result<-data.frame(Cluster=factor(Groups),GO=Annot,pvalue=as.double(pvalue),Count=as.double(counts));
    return(result);
}

gistfile2.r

DavidGOAnalysis <- function(topics,pval=0.05,path="."){
    
    require(ggplot2)    
    require(DAVIDQuery)
    DavRes<-DoDAVIDGOAnnotation(topics,pval);
    pngName<-file.path(path,"DavidGOEnrich.png");
    
    if(nrow(DavRes)){
        ggplot(DavRes, aes(x=Cluster, y=GO,colour=pvalue)) + 
            geom_point(aes(size=Count))+ 
            scale_colour_gradient(low="red", high="blue")
        
        ggsave(pngName,width=50.8,height=28.575,units="cm")
    }                            
    return(DavRes)
}