Nothing
mmds.2D.plot <- function (x,project = NULL, title = NULL, axis = c(1, 2), xlim = NULL,
ylim = NULL, outfile.type = NULL,
outfile.name = "mmds",new.plot = TRUE, active.col = x$col[,3],
active.alpha = 1, sup.col = project$col[,3], active.pch = 20,
sup.pch = 3, active.lab = FALSE, sup.lab = FALSE, active.cex = 2,
sup.cex = 2, active.legend.cex = 2, sup.legend.cex = 2,
active.legend.lwd = 1, sup.legend.lwd = 2, active.lwd = 1, sup.lwd = 4,
legend = TRUE, active.legend.pos = "bottomleft",
sup.legend.pos = "bottomright", active.legend.name = x$group[,1],
sup.legend.name = project$group[,1], active.legend.col = x$group[,2],
sup.legend.col = project$group[,2], outfile.width = NULL, outfile.height = NULL,
box.lwd = 1, cex.axis = 1, cex.lab = 1, sup.legend.text = 1,
active.legend.text = 1, legend.axis = TRUE, grid = TRUE, axes = TRUE) {
#check arguments
if (!inherits(x, "mmds"))
stop("object of class 'mmds' expected")
if (any(axis > length(x$eigen.perc)))
stop("wrong axis")
if(!is.null(project) && (!inherits(project, "project")))
stop("object of class 'project' expected")
#display eigenvalue percentages
if(legend.axis==TRUE){
x.lab <- paste("PC", axis[1], " (", round(x$eigen.perc[axis[1]],1), "%)", sep = "")
y.lab <- paste("PC", axis[2], " (", round(x$eigen.perc[axis[2]],1), "%)", sep = "")
}
else{
x.lab<-""
y.lab<-""
}
if (is.null(xlim)) {
if (is.null(project)) {
x.min <- min(x$coord[, axis[1]])
x.max <- max(x$coord[, axis[1]])
}
else {
x.min <- min(x$coord[, axis[1]], project$coord[, axis[1]])
x.max <- max(x$coord[, axis[1]], project$coord[, axis[1]])
}
xlim <- c(x.min, x.max) * 1.2
}
if (is.null(ylim)) {
if (is.null(project)) {
y.min <- min(x$coord[, axis[2]])
y.max <- max(x$coord[, axis[2]])
}
else {
y.min <- min(x$coord[, axis[2]], project$coord[, axis[2]])
y.max <- max(x$coord[, axis[2]], project$coord[, axis[2]])
}
ylim <- c(y.min, y.max) * 1.2
}
if(is.null(outfile.type)){
if (new.plot)
dev.new()
}
else {
if(outfile.type=="pdf"){
if(is.null(outfile.width)){
outfile.width<-7
outfile.height<-7
}
pdf(paste(outfile.name,"pdf",sep="."),width=outfile.width,height=outfile.height)
}
else if(outfile.type=="png"){
if(is.null(outfile.width)){
outfile.width<-7
outfile.height<-7
}
png(paste(outfile.name,"png",sep="."),width=outfile.width,height=outfile.height,units="in",res=150)
}
else if(outfile.type=="tiff"){
if(is.null(outfile.width)){
outfile.width<-7
outfile.height<-7
}
tiff(paste(outfile.name,"tiff",sep="."),width=outfile.width,height=outfile.height,units="in",res=150,compression="lzw")
}
else if(outfile.type=="postscript"){
if(is.null(outfile.width)){
outfile.width<-0
outfile.height<-0
}
postscript(paste(outfile.name,"ps",sep="."),width=outfile.width,height=outfile.height)
}
else {
stop("Wrong file format")
}
}
#print active data
plot(x$coord[, axis[1]], x$coord[, axis[2]], col = alpha(active.col, active.alpha),
pch = active.pch, cex = active.cex, lwd = active.lwd, xlab = x.lab, ylab = y.lab, xlim = xlim,
ylim = ylim,cex.lab=cex.lab,main=title,frame=FALSE,xaxt="n",yaxt="n",mgp=c(1.6,1.6,1.6))
if (axes == TRUE) {
axis(1,lwd=box.lwd,cex.axis=cex.axis)
axis(2,lwd=box.lwd,cex.axis=cex.axis)
}
if (active.lab)
text(x$coord[, axis[1]], y = x$coord[, axis[2]],
labels = rownames(x$coord), pos = 3, col = active.col)
if (legend)
legend (active.legend.pos, bg = "white", active.legend.name, pch = active.pch, pt.cex = active.legend.cex,
pt.lwd = active.legend.lwd, col=active.legend.col,title="Active data",cex=active.legend.text,box.lwd=box.lwd)
if(!is.null(project)) {
#print supplementary data
if (legend)
legend (sup.legend.pos, bg = "white", sup.legend.name, pch = sup.pch,cex=sup.legend.text,
pt.cex = sup.legend.cex, pt.lwd = sup.legend.lwd, col=sup.legend.col,title="Sup data",box.lwd=box.lwd)
points(project$coord[, axis[1]], project$coord[, axis[2]],
col = sup.col, pch = sup.pch, cex = sup.cex, lwd = sup.lwd)
if (sup.lab)
text(project$coord[, axis[1]], y = project$coord[, axis[2]],
labels = rownames(project$coord), pos = 3, col = sup.col)
}
#lastly because in the foreground
if(grid==TRUE){
abline (v = 0, lty = 2)
abline (h = 0, lty = 2)
}
box(which="plot",lty="solid",lwd=box.lwd)
if(!is.null(outfile.type)){
dev.off()
print("File created")
}
}
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