Plot_genes_gff_file.Rscript

gff=read.table("scf218.gff")
colnames(gff)=c("Chr","Source","Feature","Start","End","Score","Strand","Frame","attribute")

pos_s=70; #start position to plot gene (Y-axis)
pos_e=120 #end position to plot gene (Y-axis)
iter=round((pos_e-pos_s)/5,0) #define distance between consecutive genes (Y-axis)
pos_s_iter=pos_s
cntr=1

for(i in 1:nrow(gff))
{
  if(gff$Feature[i]=="gene")
  {
    print(pos_s_iter)
    print(cntr)
    x=gff$Attribute[i]
    gene_name=sub("ID.*Name=",x,replacement = "")
    if(gff$Strand[i]=="+")
    {
      arrows(x0=gff$Start[i],y0=pos_s_iter,x1=gff$End[i],y1=pos_s_iter,angle = 0.5,lwd=2)
      text(x=gff$Start[i]+(gff$End[i]-gff$Start[i])/2,labels = gene_name,y=5+pos_s_iter,cex=0.7,font=4)
    }
    if(gff$Strand[i]=="-")
    {
      arrows(x1=gff$Start[i],y0=pos_s_iter,x0=gff$End[i],y1=pos_s_iter,angle = 0.5,lwd=2)
      text(x=gff$Start[i]+(gff$End[i]-gff$Start[i])/2,labels = gene_name,y=5+pos_s_iter,cex=0.7,font=4)
    }
    if(cntr<=5)
    {
      pos_s_iter=pos_s_iter+iter; 
      cntr=cntr+1
    }
    if(cntr==6)
    {
      pos_s_iter=pos_s
      cntr=1
    }

  }
}