R/visTrans.R

In GenomicTools: Collection of Tools for Genomic Data Analysis

# visTrans <- function(snpGene, geneAnnot=NULL){
#  
#  if(!is.null(geneAnnot)) annotTrack <- TRUE
# 
# # Extract the genes
#   genes <- unique(as.character(snpGene[,5]))
# 
# # Get the Annotations from it 
#   annot <- geneAnnot[is.element(geneAnnot[,1],genes),]
# 
# # Input checks and cleaning
#   if(length(genes)!=nrow(annot)) warning("Not all genes have been annotated!\n")
#   removeThese <- which((is.na(snpGene[,2]))==TRUE)
#   if(length(removeThese)>0) snpGene <- snpGene[-removeThese,]
#   
# # Determine constants for the plot
#   temp <- c(snpGene[,3],annot[,3],annot[,4])
#   xlim <- c(min(temp),max(temp))  / 10^6
#   rcolors <- rainbow(1000,end=4/6)
#  
# # Determine the color of each gene (depending on the position on the chromosome)
#   geneColors <- rcolors[floor((apply(cbind(annot[,3],annot[,4]),1,mean)/10^6 - xlim[1])/ (xlim[2]-xlim[1]) * length(rcolors))]
#  
#   snpGene[,3] <- snpGene[,3] / 10^6
#   annot[,3] <- annot[,3] / 10^6
#   annot[,4] <- annot[,4] / 10^6
#   
# # Create the layout for the plot
#   if(annotTrack==TRUE)
#   {
#     layout(matrix(c(1,2),ncol=1),heights=c(1,2))
#     par(mar=c(0,4,0,2))
#   }
#   
# # Create the upper plot
#   if(annotTrack==TRUE)
#   {
#     plot(-100,-100,xlim=xlim, ylim=c(0,1), xlab="", xaxt="n", yaxt="n",ylab="")
#   } else {
#     plot(-100,-100,xlim=xlim, ylim=c(0,1), xlab=paste("Chromosomal Position"),yaxt="n",ylab="")
#   }
# 
# # Now connect the genes and the SNP 
#   for(i in 1:nrow(snpGene)){
#     temp <- snpGene[i,]
#   # Get the temporabry locations
#     thisGene <- annot[,1]==as.character(temp[,5])
#     geneLoc <- mean(as.numeric(annot[thisGene,c(3,4)]))
#     snpLoc <- snpGene[i,3]
#     ellColor <- geneColors[thisGene]
#   # Draw the ellipse 
#     gsDist <- abs(geneLoc-snpLoc)
#     draw.ellipse(mean(c(geneLoc,snpLoc)),0,gsDist/2,gsDist/(xlim[2]-xlim[1]),segment=c(0,180),border=ellColor)
#   }
# 
# # Add the genes 
# #   for(i in 1:length(genes))
# #   {
# #     rect(annot[i,3],0,annot[i,4],0.1,col="black")
# #   }
# # Add the SNPs 
# #   for(i in 1:nrow(snpGene))
# #   {
# #     rect(snpGene[i,3],0,snpGene[i,3],0.05,col="red",border="red")
# #   }
# 
#   colnames(annot) <- c("Name","Chr","Start","Stop")
#   annot[,3] <- annot[,3] * 10^6
#   annot[,4] <- annot[,4] * 10^6
#   annot <- annot[,c(2,3,4,1)]
# # Now add the lower plot  
#  if(annotTrack==TRUE)
#  {
#      par(mar=c(5,4,0,2))
#      plotGeneLocation(annot,chrInfo=2,xlim=xlim,minDistance=1.5)
#  }
# }