Nothing
plot.stMCA <-
function(x,type='v',axes=1:2,points='all',threshold=2.58,groups=NULL,col='dodgerblue4',app=0, ...) {
if(x$call$input.mca=='multiMCA') {
if(is.null(groups)) groups <- 1:x$call$ngroups
z <- x
class(z)[1] <- 'multiMCA'
plot.multiMCA(z,type,axes,points,groups,col,...)
return()
}
tit1 <- paste('Dim ',axes[1],' (',round(x$eig[[2]][axes[1]],1),'%)',sep='')
tit2 <- paste('Dim ',axes[2],' (',round(x$eig[[2]][axes[2]],1),'%)',sep='')
if (type=='v') {
cmin <- apply(x$var$coord[,axes],2,min)*1.1
cmax <- apply(x$var$coord[,axes],2,max)*1.1
clim <- cbind(cmin,cmax)
if(points=='all') condi <- 1:nrow(x$var$coord)
if (points=='besth') condi <- abs(x$var$v.test[,axes[1]])>=threshold
if (points=='bestv') condi <- abs(x$var$v.test[,axes[2]])>=threshold
if (points=='best') condi <- abs(x$var$v.test[,axes[1]])>=threshold | abs(x$var$v.test[,axes[2]])>=threshold
coord <- x$var$coord[condi,axes]
prop <- round(x$var$weight[-x$call$excl]/nrow(x$ind$coord)*2+0.5,1)[condi]
plot(coord,col='white',xlim=clim[1,],ylim=clim[2,],xlab=tit1,ylab=tit2,...)
if(app==0) text(coord,rownames(coord),col=col,cex=1)
if(app==1) text(coord,rownames(coord),col=col,cex=prop)
if(app==2) {
points(coord,pch=17,col=col,cex=prop)
text(coord,rownames(coord),pos=3,col=col,cex=1)
}
}
if (type %in% c('i','inames')) {
cmin <- apply(x$ind$coord[,axes],2,min)*1.1
cmax <- apply(x$ind$coord[,axes],2,max)*1.1
clim <- cbind(cmin,cmax)
ni <- nrow(x$ind$coord)
if(points=='all') condi <- 1:ni
if (points=='besth') condi <- x$ind$contrib[,axes[1]]>=100/ni
if (points=='bestv') condi <- x$ind$contrib[,axes[2]]>=100/ni
if (points=='best') condi <- x$ind$contrib[,axes[1]]>=100/ni | x$ind$contrib[,axes[2]]>=100/ni
coord <- x$ind$coord[condi,axes]
if(type=='i') pcol <- col
if(type=='inames') pcol <- 'white'
plot(coord,col=pcol,xlim=clim[1,],ylim=clim[2,],xlab=tit1,ylab=tit2,pch=19,cex=0.2,...)
if(type=='inames') text(coord,rownames(coord),col=col)
}
abline(h=0,v=0,col='grey')
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.