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g.princals.R
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g.princals.R
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g.princals=function(x, plot.dim = c(1, 2),var.subset= "all", max.plot.array =2,
stepvec = NA, col.lines = "black",main,
show=c(TRUE,FALSE,T,F,1,0),
save=c(TRUE,FALSE,T,F,1,0),name,
width = 300, height =300, units = 'mm',
res =480,dispersion=3,colour.group=NA,
point.size.loadplot=1,
point.alpha.loadplot=0.1,
language=c("english","spanish"),
legend.position=c("none", "left", "right", "bottom", "top"),
legend.group=c(TRUE,FALSE,T,F,1,0)){
#####################################
# License: GNU
# Author: José Solís, October 2024
# email: solisbenites.jose@gmail.com
####################################
require("Gifi")
require("ggplot2")
require("scales")
require("grid")
require("plyr")
require("gridExtra")
require("ggrepel")
require("ggh4x")
require("Hmisc")
require("RColorBrewer")
##############################################################################
##############################################################################
begin=Sys.time()#Begining time
cat(paste0("To begin to g.princals of ",deparse(substitute(x)), sep="\n\n"))
if (missing(name)) name=as.character(x$call[2])
if (missing(show)) show=1
if (missing(save)) save=0
if (missing(legend.group)) legend.group=0
if (missing(main)) main=colnames(x$data)
if (missing(var.subset)) var.subset="all"
if (missing(width)) width = 300
if (missing(height)) height =300
if (missing(units)) units = 'mm'
if (missing(res)) res =480
if (missing(dispersion)) dispersion =3
if (missing(language)) language="english"
if (missing(legend.position)) legend.position="right"
if (missing(point.size.loadplot)) point.size.loadplot=1
if (missing(point.alpha.loadplot)) point.alpha.loadplot=.1
ss=c(0,1,T,F,TRUE,FALSE)
if(length(show)!=1){
beep(7)
stop("'show' should be one item")
}else{
if(sum(ss==show)!=3){
beep(7)
stop("'show'don´t allowed, just to be TRUE,FALSE,T,F,1 and 0")
}
}
if(length(save)!=1){
beep(7)
stop("'save' should be one item")
}else{
if(sum(ss==save)!=3){
beep(7)
stop("'save' don´t allowed, just to be TRUE,FALSE,T,F,1 and 0")
}
}
if(length(legend.group)!=1){
beep(7)
stop("'legend.group' should be one item")
}else{
if(sum(ss==legend.group)!=3){
beep(7)
stop("'legend.group' don´t allowed, just to be TRUE,FALSE,T,F,1 and 0")
}
}
if(is.numeric(dispersion)<1){beep(7);stop("Dispersion of loadplot´s points should a number between 0.5 to 6")}
if((dispersion>.49&dispersion<6.01)==0){beep(7);stop("Dispersion of loadplot´s points is number between 0.5 to 6")}
if(is.numeric(point.size.loadplot)<1) {beep(7);stop("point.size.loadplot of loadplot´s points should a number between 0.01 to 3")}
if(is.numeric(point.alpha.loadplot)<1) {beep(7);stop("point.alpha.loadplot of loadplot´s points should a number between 0.01 to 1")}
if((point.size.loadplot>0&point.size.loadplot<3.01)==0) {beep(7);stop("point.size.loadplot of loadplot´s points is number between 0.01 to 3")}
if((point.alpha.loadplot>0&point.alpha.loadplot<1.01)==0) {beep(7);stop("point.alpha.loadplot of loadplot´s points is number between 0 to 1")}
if (missing(colour.group)){
col="red"
legend.group=0
}else{
if(ncol(x$data)==length(colour.group)){
col=factor(colour.group)
}else{
beep(7)
stop("number of groups shoud be the same numbers of columns")
}
}
if(length(language)!=1){
beep(7)
stop("'language' should be one item")
}else{
if(sum(c("english","spanish")==language)!=1){
beep(7)
stop("'language'don´t allowed, just to be english or spanish")
}
}
if(language=="spanish") label.language=c("Grupo de\n variables","CP ","Número de componentes","Autovalores","Observado","Transformado"," de ")
if(language=="english") label.language=c("Group of\nvariables","PC ","Number of Components","Eigenvalues","Observed","Transformed"," of ")
beep(2)
beep(2)
beep(2)#mario bros sound
################################################################################
#biplot
main=paste0("Biplot ",name)
nvar <- dim(x$data)[2]
VAF=x$evals[1:nvar]/sum(x$evals[1:nvar])
vaf=VAF[plot.dim]
xycoor=x$loadings
vPC1 <- xycoor[,1]
vPC2 <- xycoor[,2]
vlabs <- rownames(xycoor)
vPCs <- data.frame(vPC1=vPC1,vPC2=vPC2)
rownames(vPCs) <- vlabs
vPCs$col=col
# put a faint circle there, as is customary
angle <- seq(-pi, pi, length = 100)
df <- data.frame(x = sin(angle), y = cos(angle))
p1=ggplot(aes(x, y), data = df)+
theme_classic()+
geom_path(colour="grey70")+
geom_vline(aes(xintercept=0), colour="grey70", linetype="dashed")+
geom_hline(aes(yintercept=0), colour="grey70", linetype="dashed")+
scale_x_continuous(breaks =scales::pretty_breaks(n = 5),guide = "axis_minor")+
scale_y_continuous(breaks =scales::pretty_breaks(n = 5),guide = "axis_minor")+
xlab(paste0("Dim ", plot.dim[1]," (",round(vaf[1]*100,2),"%)") ) +
ylab(paste0("Dim ", plot.dim[2]," (",round(vaf[2]*100,2),"%)") )+
ggtitle(main)+
geom_segment(data=vPCs, aes(x = 0, y = 0, xend = vPC1, yend = vPC2,colour=col), arrow = arrow(length = unit(.75, 'picas')))+
scale_colour_brewer(name=label.language[1],palette="Set1")+
geom_text_repel(data= subset(vPCs,vPC1>0), aes(x=vPC1,y=vPC2,label=rownames(subset(vPCs,vPC1>0)),colour=col,segment.colour="black"),
force = .1,
nudge_x = 1.25-subset(vPCs,vPC1>0)$vPC1*.5,
direction = "y",
vjust = .5,
hjust = 0,
segment.size = .2,
segment.curvature = -.1,
min.segment.length = unit(0, 'lines'),
size=4,
fontface = 'bold',
point.padding = unit(1, 'lines'),
segment.ncp = 3,
segment.angle =45,
box.padding = unit(1, 'lines'),
max.time = 100)+
scale_colour_brewer(name=label.language[1],palette="Set1")+
geom_text_repel(data= subset(vPCs,vPC1<0), aes(x=vPC1,y=vPC2,label=rownames(subset(vPCs,vPC1<0)),segment.colour="black",colour=col),
force = .1,
nudge_x = -1.25-subset(vPCs,vPC1<0)$vPC1*.5,
direction = "y",
vjust = .5,
hjust = 1,
segment.size = .2,
segment.curvature = -.1,
min.segment.length = unit(0, 'lines'),
size=4,
fontface = 'bold',
point.padding = unit(1, 'lines'),
segment.ncp = 3,
segment.angle =45,
box.padding =unit(1, 'lines'),
max.time = 100)+
scale_colour_brewer(name=label.language[1],palette="Set1")+
coord_fixed(ratio = 1)+
theme(plot.title = element_text(size = 18, face = "bold"),
axis.text=element_text(size=12),
axis.title=element_text(size=14,face="bold"),
legend.position=legend.position,
legend.title=element_text(size=14, face = "bold"),
legend.text=element_text(size=14))+
if(legend.group==0){
theme(legend.position="none")
}else{
guides(colour = guide_legend(override.aes = aes(label ="")))
}
################################################################################
#loadplot
main=paste0("Loadplot ",name)
pxy=data.frame(x$objectscores[,1:2])
mx=mean(pxy[,1],na.rm = T)
sx=sd(pxy[,1],na.rm = T)
lx1=mx-dispersion*sx
lx2=mx+dispersion*sx
my=mean(pxy[,2],na.rm = T)
sy=sd(pxy[,2],na.rm = T)
ly1=my-dispersion*sy
ly2=my+dispersion*sy
pxy1=subset(pxy,pxy[,1]>lx1)
pxy2=subset(pxy1,pxy1[,1]<lx2)
pxy3=subset(pxy2,pxy2[,2]>ly1)
pxy4=subset(pxy3,pxy3[,2]<ly2)
l1=min(-1*max(abs(pxy4[,1]),na.rm = T)-sd(pxy4[,1],na.rm = T),-1*max(abs(pxy4[,2]),na.rm = T)-sd(pxy4[,2],na.rm = T),na.rm=T)*(1+.1/(.5*dispersion**3+dispersion))
l2=max(max(abs(pxy4[,1]),na.rm = T)+sd(pxy4[,1],na.rm = T),max(abs(pxy4[,2]),na.rm = T)+sd(pxy4[,2],na.rm = T),na.rm=T)*(1+1/(.5*dispersion**3+dispersion))
colnames(pxy4)=c("D1","D2")
p2=ggplot(data=pxy4,aes(x=D1,y=D2))+
theme_classic()+
geom_vline(aes(xintercept=0), colour="grey70", linetype="dashed")+
geom_hline(aes(yintercept=0), colour="grey70", linetype="dashed")+
geom_point(size =point.size.loadplot,alpha =point.alpha.loadplot)+
xlab(paste0(label.language[2], plot.dim[1]," (",round(vaf[1]*100,2),"%)"))+
ylab(paste0(label.language[2], plot.dim[2]," (",round(vaf[2]*100,2),"%)"))+
ggtitle(main)+
geom_segment(data=vPCs, aes(x = 0, y = 0, xend = vPC1, yend = vPC2,colour=col),arrow = arrow(length = unit(.75, 'picas')))+
scale_colour_brewer(name=label.language[1],palette="Set1")+
geom_text_repel(data= subset(vPCs,vPC1>0), aes(x=vPC1,y=vPC2,label=rownames(subset(vPCs,vPC1>0)),segment.colour="black",colour=col),
force = .1,
nudge_x =1.5-subset(vPCs,vPC1>0)$vPC1*.5,
direction = "y",
vjust = .5,
hjust = 0,
segment.size = .2,
segment.curvature = -.1,
min.segment.length = unit(0, 'lines'),
size=4,
fontface = 'bold',
point.padding = unit(1, 'lines'),
segment.ncp = 3,
segment.angle =45,
box.padding = unit(1, 'lines'),
max.time = 100)+
scale_colour_brewer(name=label.language[1],palette="Set1")+
geom_text_repel(data= subset(vPCs,vPC1<0), aes(x=vPC1,y=vPC2,label=rownames(subset(vPCs,vPC1<0)),segment.colour="black",colour=col),
force = .1,
nudge_x = -1.5-subset(vPCs,vPC1<0)$vPC1*.5,
direction = "y",
vjust = .5,
hjust = 1,
segment.size = .2,
segment.curvature = -.1,
min.segment.length = unit(0, 'lines'),
size=4,
fontface = 'bold',
point.padding = unit(1, 'lines'),
segment.ncp = 3,
segment.angle =45,
box.padding = unit(1, 'lines'),
max.time = 100)+
scale_x_continuous(limits=c(l1,l2),breaks =scales::pretty_breaks(n = 4),guide = "axis_minor")+
scale_y_continuous(limits=c(l1,l2),breaks =scales::pretty_breaks(n = 4),guide = "axis_minor")+
scale_colour_brewer(name=label.language[1],palette="Set1")+
coord_fixed(ratio = 1)+
theme(plot.title = element_text(size = 18, face = "bold"),
axis.text=element_text(size=12),
axis.title=element_text(size=14,face="bold"),
legend.position=legend.position,
legend.title=element_text(size=14, face = "bold"),
legend.text=element_text(size=14))+
if(legend.group==0){
theme(legend.position="none")
}else{
guides(colour = guide_legend(override.aes = aes(label = "")))
}
################################################################################
#screeplot
nd <-data.frame(x=1:length(x$evals),y=x$evals)
main <- paste0("Scree Plot ",name)
xlab <- label.language[3]
ylab <- label.language[4]
ylim <- c(0, max(x$evals))
p3=ggplot(nd,aes(x=x,y=y)) +
theme_classic(base_size = 20)+
geom_line(colour="blue")+geom_point(colour="blue")+
scale_x_continuous(breaks =scales::pretty_breaks(n = length(x$evals)),guide = "axis_minor")+
scale_y_continuous(limits=ylim,breaks =scales::pretty_breaks(n = round(x$evals[1]+.5)),guide = "axis_minor")+
ggtitle(main)+
xlab(xlab)+
ylab(ylab)+
theme(plot.title = element_text(size = 18, face = "bold"))
################################################################################
#transplot
xlab <- label.language[5]
ylab <- label.language[6]
main <- colnames(x$data)
if (var.subset[1] == "all") var.subset <- colnames(x$data) ## extract variables and scores to be plotted
if (is.numeric(var.subset)) var.subset <- colnames(x$data)[var.subset]
if (missing(main)) main <- var.subset
if (missing(max.plot.array)) max.plot.array=2
nvars <- length(var.subset)
vars=length(var.subset)
g=ceiling(nvars/(max.plot.array**2))
if(sum(show==TRUE,show==T,show==1,na.rm=T)==3){
print(paste0("Ok, it just shows ",name,"-transplots"))
}else{
print(paste0("Ok, just ",name,"-transplots did not show"))
}
vx=NA
vy=NA
if(nvars%%max.plot.array**2==0){
vy=seq(max.plot.array**2,nvars,by=max.plot.array**2)
vx=c(1,vy+1%%max.plot.array**2)
}else{
vy=c(seq(max.plot.array**2,nvars,by=max.plot.array**2),nvars)
vx=c(1,vy+1%%max.plot.array**2)
}
nn=data.frame(vx[1:as.numeric(g)],vy[1:as.numeric(g)])
for(k in 1:as.numeric(g)){
if(sum(save==TRUE,save==T,save==1,na.rm=T)==3){
png(filename = paste0(name,".transplot.",k,".png"),res=res,width=width,height=height,units=units)
}else{
print(paste0(name,"-Transplots, it were not saved"))
}
if (class(x$transform[,var.subset])[1] == "list") { ## homals-type transformation plot if copies are present
nvars <- length(var.subset) ## number of variables to be plotted
plotvars <- as.matrix(x$datanum[,var.subset])
xlabels <- as.data.frame(x$data[,var.subset])
ploty <- x$transform[,var.subset] ## list
ploty <- lapply(ploty, function(cc) if (ncol(cc) < length(plot.dim)) as.matrix(cc) else as.matrix(cc[, plot.dim]))
knotsv <- x$knots[var.subset]
ordv <- x$ordinal[var.subset]
if (missing(max.plot.array)) {
npanv <- ceiling(sqrt(nvars))
npanh <- floor(sqrt(nvars))
if (npanv * npanh < nvars) npanv <- npanv + 1
if (npanv == 1 && npanh == 1) parop <- FALSE else parop <- TRUE
} else {
if (length(max.plot.array) < 2){
npanv <- max.plot.array[1]
npanh <- max.plot.array[1]
} else {
npanv <- max.plot.array[1]
npanh <- max.plot.array[2]
}
npanv <- max(npanv, 1)
npanh <- max(npanh, 1)
if (npanv == 1 && npanh == 1) parop <- FALSE else parop <- TRUE
}
if (parop) op <- par(mfrow = c(npanv, npanh))
for (i in (nn[k,1]:nn[k,2])) {
img=paste0(i,label.language[7],vars)
ylims <- range(c(ploty[[i]]))*1.05
for (j in 1:ncol(ploty[[i]])) {
if (length(col.lines) < ncol(ploty[[i]])) col.lines <- 1:ncol(ploty[[i]])
x1 <- plotvars[,i]
y1 <- ploty[[i]][,j]
xy <- cbind(x1, y1)
ord <- order(xy[,1])
if (!is.factor(xlabels[,i])) xlabels[,i] <- round(xlabels[,i], 2)
if (is.na(stepvec[1])) crit <- (length(knotsv[[i]]) == (length(unique(plotvars[,i]))-2)) else crit <- stepvec[i]
if (crit) { ## plot step function
sfun0 <- stepfun(xy[ord,1][-1], xy[ord,2], f = 0)
if (ordv[i]) vert <- TRUE else vert <- FALSE
if (j == 1) {
#plot(sfun0, xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines[j], do.points = FALSE, verticals = vert, ylim = ylims, lwd = 2, ...)
plot(sfun0, xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines[j], do.points = FALSE, verticals = vert, ylim = ylims, lwd = 2)
abline(v = x1, col = "gray", lwd = 0.8)
axis(1, labels = xlabels[,i], at = x1)
axis(2, col = col.lines[j]) # formatted Y-axis
mtext(img, side = 1, line =3 , cex = 0.8, adj =.9)
minor.tick( nx = 2, ny = 2, tick.ratio = 0.5,
x.args = list(lwd = 1), # X-minor tick format argumnets
y.args = list(col = col.lines[j]))
} else {
plot(sfun0, xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines[j], do.points = FALSE,
add = TRUE, verticals = vert, lwd = 2)
}
} else {
if (j == 1) {
plot(xy[ord,1], xy[ord,2], type = "l", xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines[j],ylim = ylims, lwd = 2)
axis(1, labels = xlabels[,i], at = x1)
axis(2, col = col.lines[j]) # formatted Y-axis
minor.tick( nx = 2, ny = 2, tick.ratio = 0.5,
x.args = list(lwd = 1), # X-minor tick format argumnets
y.args = list(col = col.lines[j]))
mtext(img, side = 1, line =3 , cex = 0.8, adj =.9)
} else {
points(xy[ord,1], xy[ord,2], type = "l", col = col.lines[j], lwd = 2)
}
}
}
}
if (parop) on.exit(par(op))
} else { ## standard transformation plot with no copies
nvars <- length(var.subset) ## number of variables to be plotted
plotvars <- as.matrix(x$datanum[,var.subset])
xlabels <- as.data.frame(x$data[,var.subset])
ploty <- as.matrix(x$transform[,var.subset])
knotsv <- x$knots[var.subset]
ordv <- x$ordinal[var.subset]
if (is.na(max.plot.array)) {
npanv <- ceiling(sqrt(nvars))
npanh <- floor(sqrt(nvars))
if (npanv * npanh < nvars) npanv <- npanv + 1
if (npanv == 1 && npanh == 1) parop <- FALSE else parop <- TRUE
} else {
if (length(max.plot.array) < 2){
npanv <- max.plot.array[1]
npanh <- max.plot.array[1]
} else {
npanv <- max.plot.array[1]
npanh <- max.plot.array[2]
}
npanv <- max(npanv, 1)
npanh <- max(npanh, 1)
if (npanv == 1 && npanh == 1) parop <- FALSE else parop <- TRUE
}
if (parop) op <- par(mfrow = c(npanv, npanh))
## begin plotting
for (i in nn[k,1]:nn[k,2]) {
img=paste0(i,label.language[7],vars)
x1 <- plotvars[,i]
y1 <- ploty[,i]
xy <- cbind(x1, y1)
ord <- order(xy[,1])
if (!is.factor(xlabels[,i])) xlabels[,i] <- round(xlabels[,i], 2)
if (is.na(stepvec[1])) crit <- length(knotsv[[i]]) == (length(unique(plotvars[,i]))-2) else crit <- stepvec[i]
if (crit) { ## plot step function
sfun0 <- stepfun(xy[ord,1][-1], xy[ord,2], f = 0)
if (ordv[i]) vert <- TRUE else vert <- FALSE
plot(sfun0, xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines, do.points = FALSE, verticals = vert)
#plot(sfun0, xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines, do.points = FALSE, verticals = vert)
axis(1, labels = xlabels[,i], at = x1)
axis(2, col = col.lines)
mtext(img, side = 1, line =3 , cex = 0.8, adj =.9)
minor.tick( nx = 2, ny = 2, tick.ratio = 0.5,
x.args = list(lwd = 1), # X-minor tick format argumnets
y.args = list(col = col.lines))
} else {
plot(xy[ord,1], xy[ord,2], type = "l", xlab = xlab, ylab = ylab, main = main[i], xaxt = "n", col = col.lines)
axis(1, labels = xlabels[,i], at = x1)
axis(2, col = col.lines)
mtext(img, side = 1, line =3 , cex = 0.8, adj =.9)
minor.tick( nx = 2, ny = 2, tick.ratio = 0.5,
x.args = list(lwd = 1), # X-minor tick format argumnets
y.args = list(col = col.lines))
}
}
if (parop) on.exit(par(op))
}
if(sum(save==TRUE,save==T,save==1,na.rm=T)==3){
dev.off()
print(paste0(name,"-Transplots were saved,but you do not see plots"))
}else{
print(paste0("Watch out, ",name,"-Transplot was not save"))
}
}
if(sum(show==TRUE,show==T,show==1,na.rm=T)==3){
return(list(p3,p2,p1))
print(paste0(name,"-Biplot, loadplot and scree plots just shows"))
}else{
print(paste0("Ok, ",name,"-Biplot, loadplot and scree plots did not show"))
}
if(sum(save==TRUE,save==T,save==1,na.rm=T)==3){
ggsave(paste0(name,".biplot.png"), dpi = res, width = width,height = height,unit=units,plot =p1)
ggsave(paste0(name,".loadplot.png"), dpi = res, width = width,height = height,unit=units,plot =p2)
ggsave(paste0(name,".screeplot.png"), dpi = res, width = width,height = height,unit=units,plot =p3)
print(paste0(name,"-Biplot, loadplot and scree plots were saving"))
}else{
print(paste0("Ok, ",name,"-Biplot, loadplot and scree plots were not save"))
}
}
################################################################################
################################################################################
end=Sys.time()#ending time
tem=round(end-begin,2)
cat("Working time was estimated how", sep="\n\n")
print(tem)
cat(paste0("g.princals finished of ",deparse(substitute(x))," successfully!!", sep="\n\n"))
beep(8)#mario bros sound