plot_cyto_graph.R

#' plot_cyto_graph Function
#' 
#' This function takes the output of cyto_graph and plots the information or, given the results and the reference build, generates the information and then plots a heatmap-eaque graph.
#' @param list_from_cyto
#' cyto_list
#' ref_list
#' @keyword
#' @export
#' @examples 
#' plot_cyto_graph()
plot_cyto_graph<-function(cyto_list=NULL,list_from_cyto=NULL,ref_list="GRCh38",ylabel=NULL){
  
  if(is.null(ylabel)){
    if(length(uniq_coord_name) < 50){
      ylabel=T
    }else{
      ylabel=F
    }
  }
   if(!is.null(cyto_list))
  {
    list_from_cyto<-cyto_graph(cyto_list,ref_list)
    rect_maker<-list_from_cyto[[1]]
    xbegin<-list_from_cyto[[2]]
    xcoord_master<-list_from_cyto[[3]]
    y_above<-list_from_cyto[[4]]
    y_below<-list_from_cyto[[5]]
    sorted_reflist<-list_from_cyto[[6]]
    cum_length_coords<-list_from_cyto[[7]]
    start_cum_length<-list_from_cyto[[8]]
    uniq_coord_name<-list_from_cyto[[9]]  
  }else if(!is.null(list_from_cyto)){
    rect_maker<-list_from_cyto[[1]]
    xbegin<-list_from_cyto[[2]]
    xcoord_master<-list_from_cyto[[3]]
    y_above<-list_from_cyto[[4]]
    y_below<-list_from_cyto[[5]]
    sorted_reflist<-list_from_cyto[[6]]
    cum_length_coords<-list_from_cyto[[7]]
    start_cum_length<-list_from_cyto[[8]]
    uniq_coord_name<-list_from_cyto[[9]]  
  }
  
  
  plot.new()
  
  plot.window(c(0,1),c(0,1),mar=rep(0,4))
  
  rect(xleft=xcoord_master, xright=1,ybottom=y_below,ytop=y_above,col="gray90")
  
  if(nrow(rect_maker)>0)
  {
    apply(rect_maker,1,
          function(x){ 
            if(x[5]=="Gain")
            {
              rect(xleft=x[1], xright=x[2],ybottom=x[3],ytop=x[4],col="red",border=NA)
              
            }else if(x[5]=="Loss"){
              rect(xleft=x[1], xright=x[2],ybottom=x[3],ytop=x[4],col=rgb(0,0,1,alpha=0.5),border=NA)
              
            }else if(x[5]=="Double"){
              rect(xleft=x[1], xright=x[2],ybottom=x[3],ytop=x[4],col="orange",border=NA)
              
            }
            
          })
    
    
    ##take lines away if number of samples is over 20
    if(length(uniq_coord_name)<20)
    {
      sapply(unique((rect_maker[,3])),function(x){lines(x=c(xcoord_master,1),y=c(x[1],x[1]))})
    }
    
    if(ylabel == T)
    {
      text(x=xcoord_master,y=c(unique((rect_maker[,3]+rect_maker[,4])/2)),labels=uniq_coord_name,cex=0.8,pos=2)
    }
  }
  
  lines(x=c(xcoord_master,xcoord_master),y=c(y_above+0.02,y_above+0.08))
  sapply(cum_length_coords*(1-xcoord_master)+xcoord_master,function(x){lines(x=c(x,x),y=c(y_above+0.02,y_above+0.08));lines(x=c(x,x),y=c(y_above,y_below),col="white")})
  lines(x=c(xcoord_master,1),y=c(y_above+0.02,y_above+0.02))
  text(x=c(start_cum_length*(1-xcoord_master)+xcoord_master+as.numeric(sorted_reflist[,2])/sum(as.numeric(sorted_reflist[,2]))/2*(1-xcoord_master)),y=(y_above*2+0.1)/2,labels=gsub("chr","",sorted_reflist[,1]),cex=1,offset=0)
  
  
  rect(xleft=xcoord_master, xright=1,ybottom=y_below,ytop=y_above,col=NA)
  
  ##legend(x=0.20,y= 0.2,uniq_coord_name)
  legend(x=1,y= y_below-0.03,legend=c("Gain","Hemizygous Loss","Homozygous Loss"),fill=c("red",rgb(0,0,1,alpha=0.5),"orange"),xjust=1,yjust=1,cex=0.7)
  ##xlab("Chromosome")
  ##ylab("Sample")
}