Nothing
scatterplot <-
function(x,cpg.rank=NULL,cpg.name=NULL,save.plot=NULL,
file.type="pdf",eps.size=c(5,5),
popup.pdf=FALSE,
beta.values=NULL,
user.indep=NULL,
main.title=NULL,...) {
nam.ind<-x$info$Phenotype
if(!((x$info$betainfo) %in% ls(.GlobalEnv)) & is.null(beta.values)){
stop("\nbeta values is no longer in the environment. Either provide the new name of the beta values\n object (see help(scatterplot))",
" or reload the object\n")
}
if(is.null(x$indep)) {
if(is.null(user.indep)){
stop("No independent variable found in objects. No plots can be made\n")
}
if(!is.null(user.indep)){
x$indep<-user.indep
}
}
if(is.null(cpg.rank) & is.null(cpg.name)) {
stop("No cpg sites given. Please specify what sites you want to plot\n")
}
if(is.null(beta.values)) {y=eval(parse(text=as.character(x$info$betainfo)))}
else {y<-beta.values}
if(!is.null(cpg.rank) & !is.null(cpg.name)) {
cpg.name=NULL
warning("Used cpg.rank\n")
}
if(!is.null(cpg.rank)) {
x$results<-x$results[order(x$results$P.value),]
place<-as.character(x$results[cpg.rank,1])
if(!is.null(save.plot)) {
save.plot<-paste(save.plot,cpg.rank,sep="_")
}}
if(!is.null(cpg.name)) {
x$results<-subset(x$results,x$results$CPG.Labels %in% cpg.name)
place<-x$results$CPG.Labels
cpg.name<-place
if(!is.null(save.plot)) {
save.plot<-paste(save.plot,cpg.name,sep="_")
}
}
holder<-which(x$results[,1] %in% place)
if(!is.null(x$covariates)) {
covar<-paste(names(x$covariates),collapse=", ")
}
if(!is.null(x$chip) & !x$info$random) {
if(!is.null(x$covariates)) {
covar<-paste(covar,x$info$chipinfo,sep=" and ")}
else{
covar<-x$info$chipinfo
} }
if(x$info$logittran & !is.factor(x$indep)) {
sampvalues<-seq(min(x$indep),max(x$indep),length.out=200)
}
betasval<-t(y[place,])
h.r<-(length(place)==1 & is.matrix(y)) | is.null(dimnames(betasval))
if(h.r) {
betasval<-t(betasval)
dimnames(betasval)<-list(NULL,place)
}
if(is.null(dimnames(betasval)) & length(place)!=1) {
betasval<-t(betasval)
dimnames(betasval)<-list(1:length(betasval),place)
}
for(i in 1:length(place)){
if(!is.null(save.plot)){
if(!(file.type %in% c("eps","pdf"))) {
stop("Incorrect file type. Must be pdf or eps\n")
}
if(file.type=="eps"){
postscript(paste(save.plot[i],".eps",sep=""), horizontal = FALSE,
onefile = FALSE, paper = "special",width=eps.size[1],height=eps.size[2])
}
if(file.type=="pdf" & !popup.pdf) {
pdf(file=paste(save.plot[i],".pdf",sep=""))
}
}
titleinfo<-paste(place[i]," modeled on ",nam.ind,sep="")
if(!is.null(x$covariates) |(!x$info$random & !is.null(x$chip))) {
if(!is.null(x$covariates) & x$info$Num.Cov >4) {
titleinfo<-paste(titleinfo,"in the presense of\n",x$info$Num.Cov,"covariates")
}
else{
titleinfo<-paste(titleinfo," in the presence of:\n",covar,sep="")
}}
if(!is.null(main.title)) {
titleinfo<-paste(place[i],": ",main.title,sep="")
}
if(is.factor(x$indep)) {
boxplot(betasval[,place[i]]~x$indep,xlab=nam.ind,ylab=place[i],main=titleinfo,
sub=paste("P.value= ",format(x$results$P.value[holder[i]],digits=3)),...)
}
else{
plot(betasval[,place[i]]~x$indep,xlab=nam.ind,ylab=place[i],main=titleinfo,
sub=paste("P-value = ",format(x$results$P.value[holder[i]],digits=3)),...)
if(!x$info$logittran) {
abline(a=x$coefficients[place[i],3],b=x$coefficients[place[i],4],col="red")
}
else {
if(is.factor(place)) {place<-as.character(place)}
explogitbeta<-x$coefficients[place[i],3]+x$coefficients[place[i],4]*sampvalues
testbeta<-exp(explogitbeta)/(1+exp(explogitbeta))
points(sampvalues,testbeta,type="l",col="red")
}
}
if(!is.null(save.plot)) {
if(file.type=="eps") {
dev.off()
}
else{
if(popup.pdf) {
dev.copy2pdf(file=paste(save.plot[i],".pdf",sep=""))
}
else{
dev.off()
}
}}
cat("Press enter to continue\n")
readline()
if(i==length(place)) {
cat("All ",length(place)," sites plotted\n",sep="")
break}
}}
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