Nothing
plot.PCA.ContCont <- plot.Multivar.PCA.ContCont <- function(x, Xlab.PCA, Main.PCA, Type="Percent",
Labels=FALSE, PCA=TRUE,
Good.Pretreat=FALSE, EffectT0T1=FALSE, R2_psi_g=FALSE, Main.Good.Pretreat,
Par=par(oma=c(0, 0, 0, 0), mar=c(5.1, 4.1, 4.1, 2.1)), col, ...){
Object <- x
if (methods::is(Object, "Multivar.PCA.ContCont")==TRUE & Good.Pretreat==TRUE){
stop("A plot of delta (argument Good.Pretreat=TRUE can only be obtained for fitted objects of class PCA.ContCont.")
}
# voor uni
if (methods::is(Object, "PCA.ContCont")==TRUE){
if (missing(Xlab.PCA)) {Xlab.PCA <- expression(rho[psi])}
if (missing(Main.PCA)) {Main.PCA="PCA"}
if (missing(col)) {col <- c(8)}
if (PCA==TRUE){
dev.new()
par=Par
if (Type=="Freq"){
h <- hist(Object$PCA, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$PCA)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=T, xlab=Xlab.PCA, ylab="Frequency", col=col, main=Main.PCA, ...)
}
if (Labels==TRUE){
plot(h,freq=T, xlab=Xlab.PCA, ylab="Frequency", col=col, main=Main.PCA, labels=labs, ...)
}
}
if (Type=="Percent"){
h <- hist(Object$PCA, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$PCA)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=F, xlab=Xlab.PCA, ylab="Percentage", col=col, main=Main.PCA, ...)
}
if (Labels==TRUE){
plot(h,freq=F, xlab=Xlab.PCA, ylab="Percentage", col=col, main=Main.PCA, labels=labs, ...)
}
}
if (Type=="CumPerc"){
h <- hist(Object$PCA, breaks=length(Object$PCA), ...)
h$density <- h$counts/sum(h$counts)
cumulative <- cumsum(h$density)
plot(x=h$mids, y=cumulative, xlab=Xlab.PCA, ylab="Cumulative percentage", col=0, main=Main.PCA, ...)
lines(x=h$mids, y=cumulative)
}
}
if (Good.Pretreat==TRUE){
if (missing(Main.Good.Pretreat)) {Main.Good.Pretreat = " "}
par=Par
if (Type=="Freq"){
h <- hist(Object$GoodSurr$delta, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$GoodSurr$delta)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=T, xlab=expression(delta), ylab="Frequency", main=Main.Good.Pretreat, col=col, ...)
}
if (Labels==TRUE){
plot(h,freq=T, xlab=expression(delta), ylab="Frequency", col=col, labels=labs,
main=Main.Good.Pretreat, ...)
}
}
if (Type=="Percent"){
h <- hist(Object$GoodSurr$delta, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$GoodSurr$delta)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=F, xlab=expression(delta), ylab="Percentage", col=col, main=Main.Good.Pretreat, ...)
}
if (Labels==TRUE){
plot(h,freq=F, xlab=expression(delta), ylab="Percentage", col=col, labels=labs,
main=Main.Good.Pretreat, ...)
}
}
if (Type=="CumPerc"){
h <- hist(Object$GoodSurr$delta, breaks=length(Object$GoodSurr$delta), ...)
h$density <- h$counts/sum(h$counts)
cumulative <- cumsum(h$density)
plot(x=h$mids, y=cumulative, xlab=expression(delta), ylab="Cumulative percentage",
col=0, main=Main.Good.Pretreat, ...)
lines(x=h$mids, y=cumulative)
}
}
if (EffectT0T1==TRUE){
if (methods::is(Object, "PCA.ContCont")==TRUE){
if (length(unique(Object$Pos.Def$T0S))>1){
cat("WARNING: This plot shows PCA as a function of rho_T0T1. Rho_T0S is not constant here, so this plot may be misleading")
}
if (length(unique(Object$Pos.Def$T1S))>1){
cat("WARNING: This plot shows PCA as a function of rho_T0T1. Rho_T1S is not constant here, so this plot may be misleading")
}
plot(Object$Pos.Def$T0T1, Object$PCA, xlab=expression(rho[T0T1]),
ylab=expression(rho[psi]), col=0, ...)
lines(Object$Pos.Def$T0T1, Object$PCA)
}
}
} # einde univar
# voor multi
if (methods::is(Object, "Multivar.PCA.ContCont")==TRUE){
if (missing(Xlab.PCA)) {Xlab.PCA <- expression(R[psi]^2)}
if (missing(Main.PCA)) {Main.PCA="PCA"}
if (missing(col)) {col <- c(8)}
if (PCA==TRUE){
dev.new()
par=Par
if (Type=="Freq"){
h <- hist(Object$PCA, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$PCA)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=T, xlab=Xlab.PCA, ylab="Frequency", col=col, main=Main.PCA, ...)
}
if (Labels==TRUE){
plot(h,freq=T, xlab=Xlab.PCA, ylab="Frequency", col=col, main=Main.PCA, labels=labs, ...)
}
}
if (Type=="Percent"){
h <- hist(Object$PCA, ...)
h$density <- h$counts/sum(h$counts)
cumulMidPoint <- ecdf(x=Object$PCA)(h$mids)
labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")
if (Labels==FALSE){
plot(h,freq=F, xlab=Xlab.PCA, ylab="Percentage", col=col, main=Main.PCA, ...)
}
if (Labels==TRUE){
plot(h,freq=F, xlab=Xlab.PCA, ylab="Percentage", col=col, main=Main.PCA, labels=labs, ...)
}
}
if (Type=="CumPerc"){
h <- hist(Object$PCA, breaks=length(Object$PCA), ...)
h$density <- h$counts/sum(h$counts)
cumulative <- cumsum(h$density)
plot(x=h$mids, y=cumulative, xlab=Xlab.PCA, ylab="Cumulative percentage", col=0, main=Main.PCA, ...)
lines(x=h$mids, y=cumulative)
}
}
if (EffectT0T1==TRUE){
plot(Object$T0T1, Object$PCA, xlab=expression(rho[T0T1]),
ylab="PCA", col=0, ...)
lines(Object$T0T1, Object$PCA)
}
if (R2_psi_g==TRUE){
par(mar=c(5.1, 5.1, 4.1, 2.1))
plot(Object$T0T1, Object$R2_psi_g$R2_psi_g, xlab=expression(rho[T0T1]),
ylab=expression(R[psi*g]^2), col=0, ...)
lines(Object$T0T1, Object$R2_psi_g$R2_psi_g)
par(mar=c(5.1, 4.1, 4.1, 2.1))
}
}
}
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