# dev.off()
#}
-PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NUL) {
+PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL) {
if (col) {
if (what == 'coord') {
rowcoord <- as.matrix(afc$colcoord)
if (!col) {
classes <- as.matrix(apply(chitable,1,which.max))
cex.par <- norm.vec(apply(chitable,1,max), 0.8,3)
- row.keep <- select.chi.classe(chitable, 60)
+ row.keep <- select.chi.classe(chitable, 80)
rowcoord <- rowcoord[row.keep,]
classes <- classes[row.keep]
cex.par <- cex.par[row.keep]
classes <- 1:clnb
cex.par <- rep(1,clnb)
}
+ if (is.null(xmin)) {
+ table.in <- rowcoord
+ xminmax <- c(min(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,1], na.rm = TRUE)), max(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,1], na.rm = TRUE)))
+ xmin <- xminmax[1]
+ xmax <- xminmax[2]
+ yminmax <- c(min(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,2], na.rm = TRUE)), max(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,2], na.rm = TRUE)))
+ ymin <- yminmax[1]
+ ymax <- yminmax[2]
+ }
#ntabtot <- cbind(rowcoord, classes)
#if (!col) ntabtot <- ntabtot[row_keep,]
xlab <- paste('facteur ', x, ' -')
open_file_graph(filename, width = width, height = height)
par(cex=PARCEX)
-
table.in <- rowcoord[order(cex.par, decreasing = TRUE),]
classes <- classes[order(cex.par, decreasing = TRUE)]
cex.par <- cex.par[order(cex.par, decreasing = TRUE)]
- table.in <- stopoverlap(table.in, cex.par=cex.par)
+ table.out <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax))
+ table.in <- table.out$toplot
+ notplot <- table.out$notplot
+ if (! is.null(notplot)) {
+ write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = ''))
+ }
classes <- classes[table.in[,4]]
cex.par <- cex.par[table.in[,4]]
make_afc_graph(table.in, classes, clnb, xlab, ylab, cex.txt = cex.par, xminmax=c(xmin,xmax), yminmax=c(ymin,ymax))
-
+ xyminmax <- list(yminmax = c(ymin,ymax), xminmax = c(xmin,xmax))
+ xyminmax
#plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
#abline(h=0,v=0)
#for (i in 1:clnb) {
.Call("is_overlap",x11,y11,sw11,sh11,boxes1)
}
########################################################
-stopoverlap <- function(x, cex.par = NULL) {
+stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
#from wordcloud
library(wordcloud)
tails <- "g|j|p|q|y"
thetaStep <- .1
rStep <- .5
toplot <- NULL
+ notplot <- NULL
# plot.new()
- plot(x[,1],x[,2], pch='')
+ plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim)
words <- rownames(x)
if (is.null(cex.par)) {
y1<- x[i,2]
wid <- strwidth(words[i],cex=size[i])
ht <- strheight(words[i],cex=size[i])
- ht <- (ht + ht*.2) + .01
- wid <- (wid + wid*.1) + .01
isOverlaped <- TRUE
while(isOverlaped){
if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
} else {
if(r>sqrt(.5)){
print(paste(words[i], "could not be fit on page. It will not be plotted."))
+ notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2]))
isOverlaped <- FALSE
}
theta <- theta+thetaStep
}
}
row.names(toplot) <- words[toplot[,4]]
- return(toplot)
+ return(list(toplot = toplot, notplot = notplot))
}
###############################################################################
}
make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
- if (is.null(xminmax)) {
- xminmax <- c(min(toplot[,1], na.rm = TRUE) + (0.1 * min(toplot[,1], na.rm = TRUE)), max(toplot[,1], na.rm = TRUE) + (0.1 * max(toplot[,1], na.rm = TRUE)))
- }
- if (is.null(yminmax)) {
- yminmax <- c(min(toplot[,2], na.rm = TRUE) + (0.1 * min(toplot[,2], na.rm = TRUE)), max(toplot[,2], na.rm = TRUE) + (0.1 * max(toplot[,2], na.rm = TRUE)))
- }
- rain <- rainbow(clnb)
+
+ rain <- rainbow(clnb)
compt <- 1
tochange <- NULL
for (my.color in rain) {
}
}
+plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) {
+ library(ape)
+ library(wordcloud)
+ classes<-classes[classes!=0]
+ classes<-as.factor(classes)
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
+ sum.cl<-(sum.cl/colSums(sum.cl)*100)
+ sum.cl<-round(sum.cl,2)
+ sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
+ sum.cl <- sum.cl[,1]
+ tree.order<- as.numeric(tree$tip.label)
+ vec.mat<-NULL
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ #ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ vec.mat <- matrix(1, nrow = 2, ncol = length(sum.cl))
+ vec.mat[2,] <- 2:(length(sum.cl)+1)
+ layout(matrix(vec.mat, nrow=2, ncol=length(sum.cl)),heights=c(1,4))
+ if (! bw) {
+ col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ }
+ par(mar=c(1,0,0,0))
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0)
+ for (i in tree.order) {
+ par(mar=c(0,0,1,0),cex=0.7)
+ #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i])
+ yval <- 1.1
+ plot(0,0,pch='', axes = FALSE)
+ vcex <- norm.vec(lclasses[[i]], 0.8, 3)
+ for (j in 1:length(lclasses[[i]])) {
+ yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02)
+ text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0)
+ }
+ }
+
+}
+
+plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) {
+ library(wordcloud)
+ library(ape)
+ classes<-classes[classes!=0]
+ classes<-as.factor(classes)
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
+ sum.cl<-(sum.cl/colSums(sum.cl)*100)
+ sum.cl<-round(sum.cl,2)
+ sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
+ sum.cl <- sum.cl[,1]
+ tree.order<- as.numeric(tree$tip.label)
+ vec.mat<-NULL
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1)
+ v<-2
+ for (i in 1:length(sum.cl)) {
+ vec.mat<-append(vec.mat,v)
+ v<-v+1
+ }
+ layout(matrix(vec.mat,length(sum.cl),2),widths=c(1,2))
+ if (! bw) {
+ col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ }
+ par(mar=c(0,0,0,0))
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(4, 0.8), random.order=FALSE, colors = colcloud[i])
+ }
+}
+
plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) {
classes<-classes[classes!=0]
classes<-as.factor(classes)
- sum.cl<-as.matrix(summary(classes))
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
sum.cl<-(sum.cl/colSums(sum.cl)*100)
sum.cl<-round(sum.cl,2)
sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
tree.order<- as.numeric(tree$tip.label)
+
+
if (! bw) {
- col = rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)]
+ col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)]
col.bars <- col
col.pie <- rainbow(nrow(sum.cl))
#col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
projects / iramuteq / blobdiff