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#####################################################################
#
# mqmcircleplot.R
#
# Copyright (c) 2009-2011, Danny Arends
#
# Modified by Pjotr Prins and Karl Broman
#
#
# first written Februari 2009
# last modified May 2011
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but without any warranty; without even the implied warranty of
# merchantability or fitness for a particular purpose. See the GNU
# General Public License, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: mqmplot_c
# mqmplotcircle
# mqmplot_circle
# circlelocations
# drawspline
# getchromosomelength
# getgenomelength
# locationtocircle
# drawcirculargenome
# loopthroughmulti
#
#
#####################################################################
mqmplot.circle <- function(cross, result, highlight=0, spacing=25, interactstrength=2,legend=FALSE, verbose=FALSE, transparency=FALSE){
if(is.null(cross)){
stop("No cross object. Please supply a valid cross object.")
}
retresults <- NULL
lod<-FALSE
if(any(class(result)=="mqmmulti")){
if(highlight > 0){
templateresult <- mqmextractmarkers(result[[highlight]])
lod<-TRUE
}else{
templateresult <- mqmextractmarkers(result[[1]])
lod<-FALSE
}
}else{
templateresult <- mqmextractmarkers(result)
lod<-TRUE
}
if(!("scanone" %in% class(templateresult))){
stop("Wrong type of result file, please supply a valid scanone object.")
}
if(transparency){
colorz <- rainbow(length(result),alpha=0.8)
}else{
colorz <- rainbow(length(result))
}
if(!legend){
totallength <- getgenomelength(templateresult)
nchr <- length(unique(templateresult[,1]))
cvalues <- circlelocations(totallength+(nchr*spacing))
drawcirculargenome(templateresult,spacing=spacing,lodmarkers=lod)
if(any(class(result)=="mqmmulti")){
#multiple scan results, so plot em all
todo <- 1:length(result)
if(highlight!=0){
#Unless we highlight only one of them
todo <- highlight
}
for(x in todo){
model <- mqmgetmodel(result[[x]])
if(!is.null(model)){
if(verbose) cat("Model found for trait ",x,"\n")
if(!is.null(cross$locations)){
if(verbose) cat("Locations of traits available\n")
location <- as.numeric(cross$locations[[x]])
traitl <- locationtocircle(templateresult,location[1],location[2],spacing=spacing)
}else{
if(verbose) cat("Locations of traits not available\n")
traitl <- t(c(0,0+0.25*(0.5-(x/length(result)))))
}
if(highlight==0){
col=colorz[x]
}else{
col=rgb(0.1, 0.1, 0.1, 0.1)
if(highlight==x) title(main = paste("Circleplot of:",colnames(cross$pheno)[x]))
}
for(y in 1:length(model[[4]])){
qtll <- locationtocircle(templateresult,model[[4]][y],model[[5]][y],spacing=spacing)
if(highlight==x){
for(z in y:length(model[[4]])){
if(!z==y){
cross <- sim.geno(cross)
eff <- effectplot(cross,pheno.col=x,mname1=model$name[y],mname2=model$name[z],draw=FALSE)
changeA <- (eff$Means[1,2]-eff$Means[1,1])
changeB <- (eff$Means[2,2]-eff$Means[2,1])
#interaction
qtl2 <- locationtocircle(templateresult,model[[4]][z],model[[5]][z],spacing=spacing)
if(!is.na(changeA) && !is.na(changeB) && !any(is.na(eff$SEs))){
col <- "blue"
if(changeA/abs(changeA) < changeB/abs(changeB)) col <- "green"
if(abs(abs(changeA)-abs(changeB)) > interactstrength*mean(eff$SEs)){
retresults <- rbind(retresults,c(model$name[y],model$name[z],changeA,changeB,mean(eff$SEs)))
drawspline(qtll,qtl2,lwd=2,col=col)
}
}
}
}
}
if(highlight==0){
points(traitl,col=col,pch=24,cex=1)
drawspline(traitl,qtll,col=col)
points(qtll*(1+0.1*((x/length(result)))),col=col,pch=19,cex=1)
}
}
}else{
if(verbose) cat("Trait ",x," has no model\n")
}
}
legend("topleft",c("Trait","QTL"),col=c("black","black"),pch=c(24,19),cex=1)
}
if(any(class(result)=="scanone") || highlight > 0){
#single scan result or highlighting one of the multiple
if(!any(class(result)=="scanone")){
#Just highlight the template result
result <- templateresult
}
model <- mqmgetmodel(result)
if(!is.null(model)){
for(y in 1:length(model[[4]])){
qtll <- locationtocircle(templateresult,model[[4]][y],model[[5]][y],spacing=spacing)
points(qtll,col="red",pch=19,cex=1)
text(qtll*1.15,model[[2]][y],col="red",cex=0.7)
if(!is.null(cross$locations)){
location <- as.numeric(cross$locations[[highlight]])
traitl <- locationtocircle(templateresult,location[1],location[2],spacing=spacing)
points(traitl,col="red",lwd=2,pch=24,cex=1.5)
}else{
traitl <- c(0,0)
}
if(!(highlight>0))drawspline(traitl,qtll,col="red")
}
}
legend("topright",c("Selected Cofactor Cofactor","Epistasis (+)","Epistasis (-)"),col=c("red","blue","green"),pch=19,lwd=c(0,1,2),cex=0.75)
legend("bottomright",c("Lod 3","Lod 6","Lod 9","Lod 12"),pch=19,lwd=0,pt.cex=c(1,2,3,4))
if(highlight==0) title(sub = "Single trait")
}
}else{
plot(c(-1,1), c(-1, 1), type = "n", axes = FALSE, xlab = "", ylab = "")
title(main = "Legend to circular genome plot")
legend("center",paste(colnames(cross$pheno)),col=colorz,pch=19,cex=0.75)
}
if(!is.null(retresults)){
colnames(retresults) <- c("Marker","Marker","Change","Change","SEs")
retresults <- as.data.frame(retresults, stringsAsFactors=TRUE)
return(invisible(retresults))
}
}
circlelocations <- function(nt){
medpoints <- matrix(nrow = nt, ncol = 2)
phi <- seq(0, 2 * pi, length = (nt + 1))
complex.circle <- complex(modulus = 1, argument = phi)
for (j in 1:nt) {
medpoints[j, ] <- c(Im(complex.circle[j]), Re(complex.circle[j]))
}
medpoints
}
drawspline <- function (cn1, cn2, lwd = 1,col="blue",...){
x <- cbind(cn1[1],0,cn2[1])
y <- cbind(cn1[2],0,cn2[2])
r <- xspline(x, y, lty=1, shape=1, lwd=lwd, border=col,...)
}
getchromosomelength <- function(result, chr){
l <- ceiling(max(result[which(result[,1]==chr),2]))
l
}
getgenomelength <- function(result){
l <- 1
for(x in unique(result[,1])){
l <- l + getchromosomelength(result,x)
}
l
}
locationtocircle <- function(result, chr, loc, spacing=50, fixoutofbounds=TRUE, verbose=FALSE){
templateresult <- result
totallength <- getgenomelength(result)
nchr <- length(unique(templateresult[,1]))
cvalues <- circlelocations(totallength+(nchr*spacing))
l <- 1
for(x in unique(templateresult[,1])){
if(x==chr){
if(loc < getchromosomelength(result,x)){
return(t(cvalues[(l+loc),]))
}else{
if(verbose) cat("Location out of chromosome bounds",loc," ",getchromosomelength(result,x),"\n")
if(fixoutofbounds) return(t(cvalues[(l+getchromosomelength(result,x)),]))
stop(paste("Location out of chromosome bounds",loc," ",getchromosomelength(result,x),"\n"))
}
}
l <- l + getchromosomelength(result,x) + spacing
}
stop("No such chromosome")
}
drawcirculargenome <- function(result,lodmarkers=FALSE,spacing=50){
result <- mqmextractmarkers(result)
plot(c(-1.1, 1.1), c(-1.1, 1.1), type = "n", axes = FALSE, xlab = "", ylab = "")
totallength <- getgenomelength(result)
nchr <- length(unique(result[,1]))
cvalues <- circlelocations(totallength+(nchr*spacing))
l <- 1
for(x in unique(result[,1])){
#Draw chromosomes
nl <- l+getchromosomelength(result,x)
lines(cvalues[l:nl,],cex=0.01)
l <- nl + spacing
}
for(x in 1:nrow(result)){
#Draw markers
if(lodmarkers){
points(locationtocircle(result,result[x,1],result[x,2],spacing=spacing),pch=20,cex=min(c((result[x,3]),4)))
}else{
points(locationtocircle(result,result[x,1],result[x,2],spacing=spacing),pch=20)
}
}
for(x in 1:nchr){
chrnumberloc <- locationtocircle(result,x,getchromosomelength(result,x)/2,spacing=spacing)
points(t(c(-1.1, -1.15)))
points(t(c(-0.9, -1.15)))
points(t(c(-0.7, -1.15)))
text(t(c(-0.9, -1.0)),paste("Distances in cM"),cex=0.8)
text(t(c(-1.1, -1.1)),paste("0 cM"),cex=0.7)
text(t(c(-0.9, -1.1)),paste(round((totallength+(nchr*spacing))*(0.2/(2*pi)),digits=1),"cM"),cex=0.7)
text(t(c(-0.7, -1.1)),paste(round((totallength+(nchr*spacing))*(0.4/(2*pi)),digits=1),"cM"),cex=0.7)
text(0.9*chrnumberloc,paste("Chr",x),cex=0.8)
}
}
loopthroughmulti <- function(cross,result,save=FALSE,spacing=100){
n <- 1
while(n <= length(result)){
if(save) png(filename=paste("circleplotT",n,".png",sep=""),width=1024,height=768)
mqmplot.circle(cross,result,spacing=spacing,highlight=n)
if(save) dev.off()
n <- n+1
}
}
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