# This function was removed and stays here commented in case it should come back...
# 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)
# }
# }
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