R/get_bubbleplot.R

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

get_bubbleplot <-
function(Xmat, GroupBy=FALSE,xlab.name="X",ylab.name="Y",cex.plots=0.8,newdevice=TRUE,
                         
                         filename="bubbleplot",file.format="pdf",
                         
                         plot.width=8,plot.height=8,plot.res=300,color.scale=c("blue","red"),statistic.type="pvalue",
                         
                         reverse.yaxis=FALSE,sizerange=c(0.01,6)){
  
  options(warn=-1)
  
  
  
  Xmat<-as.data.frame(Xmat)
  
  if(GroupBy==TRUE){
    
    
    
    colnames(Xmat)<-c("X","Y","Statistic","GroupBy")
    
  }else{
    
    colnames(Xmat)<-c("X","Y","Statistic")
    
    
    
  }
  
  
  
  Xmat$Statistic<-as.numeric(as.character(Xmat$Statistic))
  
 # print(head(Xmat))
  
  #save(Xmat,file="Xmat.Rda")
  
  
  
  if(statistic.type=="pvalue"){
    
    p=ggplot(Xmat,
             
             aes(x = X, y = Y)) +  suppressWarnings(geom_point(aes(size = abs(Statistic)), pch = 21, show.legend= TRUE))
    
  }else{
    
   
    if(statistic.type=="correlation"){
      
      p=ggplot(Xmat,
               
               aes(x = X, y = Y)) +  suppressWarnings(geom_point(aes(size = abs(Statistic)), pch = 21, show.legend= TRUE))
      
    }else{
      
      
      
      p=ggplot(Xmat,
               
               aes(x = X, y = Y)) +  suppressWarnings(geom_point(aes(size = abs(Statistic)), pch = 21, show.legend= TRUE))
      
    }
    
  }
  
  if(GroupBy==TRUE){
    
    p=p+  facet_wrap(~ GroupBy, scale="free_x",nrow=1)
    
    
    
  }
  
  p=p+labs(x=xlab.name,y=ylab.name)
  
  p=p +aes(fill = Statistic) + theme_bw()
  
  p=p+scale_fill_gradient2(low=color.scale[1],mid="white",high=color.scale[2])+scale_size(range=sizerange)
  
  
  
  #scale_size(range=c(floor(min(abs(Xmat$Statistic),na.rm=TRUE)),ceiling(max(abs(Xmat$Statistic),na.rm=TRUE))))
  
  
  
  #scale_size(range = c(0.5, 12)
  
  
  
  p=p+theme(panel.border = element_blank(), panel.grid.major = element_blank(),
            
            panel.grid.minor = element_blank(),
            
            panel.spacing=unit(1,"lines"),
            
            axis.line = element_line(colour = "black",size=1),
            
            axis.text= element_text(size=14*cex.plots), axis.title=element_text(size=18*cex.plots,face="bold"),
            
            plot.title = element_text(hjust = 0.5,size=18*cex.plots),
            
            axis.ticks.length = unit(-0.05, "in"),
            
            axis.text.y = element_text(margin=unit(c(0.3,0.3,0.3,0.3), "cm")),
            
            axis.text.x = element_text(margin=unit(c(0.3,0.3,0.3,0.3), "cm")),
            
            axis.ticks.x = element_blank(),
            
            # aspect.ratio = 1,
            
            strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
            
            strip.text = element_text(face="bold")) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
  
  
  
  #p=p+scale_fill_manual(values = c("blue","red"))
  
  
  
  if(reverse.yaxis==TRUE){
    
    p=p+scale_y_discrete(limits=rev)
    
  }
  
  p=p+theme(axis.title = element_blank())
  
  if(newdevice==TRUE){
    
    
    
    if(file.format=="pdf"){
      
      fname=paste(filename,".pdf",sep="")
      
      pdf(fname,width=plot.width,height=plot.height)
      
    }else{
      
      fname=paste(filename,".png",sep="")
      
      png(fname,width=plot.width,height=plot.height,res=plots.res,type="cairo",units="in")
      
    }
    
    print(p)
    
    dev.off()
    
  }else{
    
    #print(p)
    
  }
  
  
  
  options(warn=0)
  
  return(p)
  
}