############FIXME##################
-PlotDendroComp <- function(chd,filename,reso) {
- jpeg(filename,res=reso)
- par(cex=PARCEX)
- plot(chd,which.plots=2, hang=-1)
- dev.off()
-}
-
-PlotDendroHori <- function(dendrocutupper,filename,reso) {
- jpeg(filename,res=reso)
- par(cex=PARCEX)
- nP <- list(col=3:2, cex=c(0.5, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
- plot(dendrocutupper,nodePar= nP, edgePar = list(col='gray', lwd=2),horiz=TRUE, center=FALSE)
- dev.off()
-}
+#PlotDendroComp <- function(chd,filename,reso) {
+# jpeg(filename,res=reso)
+# par(cex=PARCEX)
+# plot(chd,which.plots=2, hang=-1)
+# dev.off()
+#}
+#
+#PlotDendroHori <- function(dendrocutupper,filename,reso) {
+# jpeg(filename,res=reso)
+# par(cex=PARCEX)
+# nP <- list(col=3:2, cex=c(0.5, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
+# plot(dendrocutupper,nodePar= nP, edgePar = list(col='gray', lwd=2),horiz=TRUE, center=FALSE)
+# dev.off()
+#}
PlotDendroCut <- function(chd,filename,reso,clusternb) {
h.chd <- as.hclust(chd)
dev.off()
}
-PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
- if (Sys.info()["sysname"]=='Darwin') {
- width<-width/74.97
- height<-height/74.97
- quartz(file=filename,type='jpeg',width=width,height=height)
- } else {
- jpeg(filename,width=width,height=height,quality=quality,res=reso)
- }
- par(cex=PARCEX)
- plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
- dev.off()
-}
+#PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
+# if (Sys.info()["sysname"]=='Darwin') {
+# width<-width/74.97
+# height<-height/74.97
+# quartz(file=filename,type='jpeg',width=width,height=height)
+# } else {
+# jpeg(filename,width=width,height=height,quality=quality,res=reso)
+# }
+# par(cex=PARCEX)
+# plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
+# dev.off()
+#}
-PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=800, height=800, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL) {
+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, active = TRUE) {
if (col) {
if (what == 'coord') {
rowcoord <- as.matrix(afc$colcoord)
}
x <- axetoplot[1]
y <- axetoplot[2]
-
if (col)
rownames(rowcoord) <- afc$colnames
if (!col){
}
clnb <- ncol(chisqrtable)
- if (!col) classes <- as.matrix(apply(chitable,1,which.max))
- else classes <- 1:clnb
- ntabtot <- cbind(rowcoord, classes)
+ 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, 80, active=active)
+ rowcoord <- rowcoord[row.keep,]
+ classes <- classes[row.keep]
+ cex.par <- cex.par[row.keep]
+ } else {
+ 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, ' -')
+ ylab <- paste('facteur ', y, ' -')
+ xlab <- paste(xlab,round(afc_table$facteur[x,2],2),sep = ' ')
+ xlab <- paste(xlab,' %%',sep = '')
+ ylab <- paste(ylab,round(afc_table$facteur[y,2],2),sep = ' ')
+ ylab <- paste(ylab,' %%',sep = '')
+
open_file_graph(filename, width = width, height = height)
par(cex=PARCEX)
- plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
- abline(h=0,v=0)
- for (i in 1:clnb) {
- ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
- if (nrow(ntab) != 0)
- text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
- }
- dev.off()
+ 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.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) {
+ # ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
+ # if (nrow(ntab) != 0)
+ # text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
+ #}
+ #dev.off()
}
filename.to.svg <- function(filename) {
open_file_graph <- function (filename, width=800, height = 800, quality = 100, svg = FALSE) {
if (Sys.info()["sysname"] == 'Darwin') {
- width <- width/74.97
- height <- height/74.97
- quartz(file = filename, type = 'jpeg', width = width, height = height)
+ width <- width/74.97
+ height <- height/74.97
+ if (!svg) {
+ quartz(file = filename, type = 'png', width = width, height = height)
+ } else {
+ svg(filename.to.svg(filename), width=width, height=height)
+ }
} else {
- #print('ATTENTION SVG!!!!!!!!!!!!!!!!!!!!!!!!!!!')
- #library(RSvgDevice)
if (svg) {
svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
} else {
}
}
+#################################################@@
+#from wordcloud
+overlap <- function(x1, y1, sw1, sh1, boxes) {
+ use.r.layout <- FALSE
+ if(!use.r.layout)
+ return(.overlap(x1,y1,sw1,sh1,boxes))
+ s <- 0
+ if (length(boxes) == 0)
+ return(FALSE)
+ for (i in c(last,1:length(boxes))) {
+ bnds <- boxes[[i]]
+ x2 <- bnds[1]
+ y2 <- bnds[2]
+ sw2 <- bnds[3]
+ sh2 <- bnds[4]
+ if (x1 < x2)
+ overlap <- x1 + sw1 > x2-s
+ else
+ overlap <- x2 + sw2 > x1-s
+
+ if (y1 < y2)
+ overlap <- overlap && (y1 + sh1 > y2-s)
+ else
+ overlap <- overlap && (y2 + sh2 > y1-s)
+ if(overlap){
+ last <<- i
+ return(TRUE)
+ }
+ }
+ FALSE
+}
+
+.overlap <- function(x11,y11,sw11,sh11,boxes1){
+ .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
+}
+########################################################
+stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
+#from wordcloud
+ library(wordcloud)
+ tails <- "g|j|p|q|y"
+ rot.per <- 0
+ last <- 1
+ thetaStep <- .1
+ rStep <- .5
+ toplot <- NULL
+ notplot <- NULL
+
+# plot.new()
+ plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim)
+
+ words <- rownames(x)
+ if (is.null(cex.par)) {
+ size <- rep(0.9, nrow(x))
+ } else {
+ size <- cex.par
+ }
+ #cols <- rainbow(clnb)
+ boxes <- list()
+ for (i in 1:nrow(x)) {
+ rotWord <- runif(1)<rot.per
+ r <-0
+ theta <- runif(1,0,2*pi)
+ x1<- x[i,1]
+ y1<- x[i,2]
+ wid <- strwidth(words[i],cex=size[i])
+ ht <- strheight(words[i],cex=size[i])
+ isOverlaped <- TRUE
+ while(isOverlaped){
+ if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
+ toplot <- rbind(toplot, c(x1, y1, size[i], i))
+ #text(x1,y1,words[i],cex=size[i],offset=0,srt=rotWord*90,
+ # col=cols[classes[i]])
+ boxes[[length(boxes)+1]] <- c(x1-.5*wid,y1-.5*ht,wid,ht)
+ isOverlaped <- FALSE
+ } 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], size[i], i))
+ isOverlaped <- FALSE
+ }
+ theta <- theta+thetaStep
+ r <- r + rStep*thetaStep/(2*pi)
+ x1 <- x[i,1]+r*cos(theta)
+ y1 <- x[i,2]+r*sin(theta)
+ }
+ }
+ }
+ nbnot <- nrow(notplot)
+ print(paste(nbnot, ' not plotted'))
+ row.names(toplot) <- words[toplot[,4]]
+ return(list(toplot = toplot, notplot = notplot))
+}
+###############################################################################
+
+getwordcloudcoord <- function(words,freq,scale=c(4,.5),min.freq=3,max.words=Inf,random.order=TRUE,random.color=FALSE,
+ rot.per=.1,colors="black",ordered.colors=FALSE,use.r.layout=FALSE,fixed.asp=TRUE,...) {
+ tails <- "g|j|p|q|y"
+ last <- 1
+
+ overlap <- function(x1, y1, sw1, sh1) {
+ if(!use.r.layout)
+ return(.overlap(x1,y1,sw1,sh1,boxes))
+ s <- 0
+ if (length(boxes) == 0)
+ return(FALSE)
+ for (i in c(last,1:length(boxes))) {
+ bnds <- boxes[[i]]
+ x2 <- bnds[1]
+ y2 <- bnds[2]
+ sw2 <- bnds[3]
+ sh2 <- bnds[4]
+ if (x1 < x2)
+ overlap <- x1 + sw1 > x2-s
+ else
+ overlap <- x2 + sw2 > x1-s
+
+ if (y1 < y2)
+ overlap <- overlap && (y1 + sh1 > y2-s)
+ else
+ overlap <- overlap && (y2 + sh2 > y1-s)
+ if(overlap){
+ last <<- i
+ return(TRUE)
+ }
+ }
+ FALSE
+ }
+
+ ord <- rank(-freq, ties.method = "random")
+ words <- words[ord<=max.words]
+ freq <- freq[ord<=max.words]
+
+
+ ord <- order(freq,decreasing=TRUE)
+ words <- words[ord]
+ freq <- freq[ord]
+ words <- words[freq>=min.freq]
+ freq <- freq[freq>=min.freq]
+ if (ordered.colors) {
+ colors <- colors[ord][freq>=min.freq]
+ }
+
+ thetaStep <- .1
+ rStep <- .05
+ plot.new()
+
+ normedFreq <- freq/max(freq)
+ size <- (scale[1]-scale[2])*normedFreq + scale[2]
+ boxes <- list()
+ toplot <- NULL
+
+
+ for(i in 1:length(words)){
+ rotWord <- runif(1)<rot.per
+ r <-0
+ theta <- runif(1,0,2*pi)
+ x1<-.5
+ y1<-.5
+ wid <- strwidth(words[i],cex=size[i],...)
+ ht <- strheight(words[i],cex=size[i],...)
+ #mind your ps and qs
+ if(grepl(tails,words[i]))
+ ht <- ht + ht*.2
+ if(rotWord){
+ tmp <- ht
+ ht <- wid
+ wid <- tmp
+ }
+ isOverlaped <- TRUE
+ while(isOverlaped){
+ if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht) &&
+ x1-.5*wid>0 && y1-.5*ht>0 &&
+ x1+.5*wid<1 && y1+.5*ht<1){
+ toplot <- rbind(toplot, c(x1,y1,size[i], i))
+ boxes[[length(boxes)+1]] <- c(x1-.5*wid,y1-.5*ht,wid,ht)
+ isOverlaped <- FALSE
+ }else{
+ if(r>sqrt(.5)){
+ warning(paste(words[i],
+ "could not be fit on page. It will not be plotted."))
+ isOverlaped <- FALSE
+ }
+ theta <- theta+thetaStep
+ r <- r + rStep*thetaStep/(2*pi)
+ x1 <- .5+r*cos(theta)
+ y1 <- .5+r*sin(theta)
+ }
+ }
+ }
+ toplot <- cbind(toplot,norm.vec(freq[toplot[,4]], 1, 50))
+ row.names(toplot) <- words[toplot[,4]]
+ toplot <- toplot[,-4]
+ return(toplot)
+}
+
+new_tree_tot <- function(chd) {
+ lf <- chd$list_fille
+ m <- matrix(0, ncol=2)
+ for (val in 1:length(lf)) {
+ if (! is.null(lf[[val]])) {
+ print(c(val,lf[[val]][1]))
+ m <- rbind(m, c(val,lf[[val]][1]))
+ m <- rbind(m, c(val,lf[[val]][2]))
+ }
+ }
+ m[-1,]
+}
+
make_tree_tot <- function (chd) {
library(ape)
lf<-chd$list_fille
dendro <- gsub('a','',dendro)
dendro_tot_cl <- read.tree(text = dendro)
#FIXME
- for (i in 1:10) {
+ for (i in 1:100) {
for (cl in 1:clnb) {
dendro <- gsub(paste('\\(',cl,',',cl,'\\)',sep=''),cl,dendro)
}
}
- for (i in 1:10) {
+ for (i in 1:100) {
dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro)
for (cl in 1:clnb) {
dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro)
row_keep
}
+select.chi.classe <- function(tablechi, nb, active = TRUE) {
+ rowkeep <- NULL
+ if (active & !is.null(debsup)) {
+ tablechi <- tablechi[1:(debsup-1),]
+ }
+ if (nb > nrow(tablechi)) {
+ nb <- nrow(tablechi)
+ }
+ for (i in 1:ncol(tablechi)) {
+ rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
+ }
+ rowkeep <- unique(rowkeep)
+ rowkeep
+}
+
+select.chi.classe.et <- function(tablechi, nb){
+ rowkeep <- NULL
+ if (!is.null(debet)) {
+ ntablechi <- tablechi[debet:nrow(tablechi),]
+ }
+ if (nb > nrow(ntablechi)) {
+ nb <- nrow(ntablechi)
+ }
+ for (i in 1:ncol(ntablechi)) {
+ rowkeep <- append(rowkeep,order(ntablechi[,i], decreasing = TRUE)[1:nb])
+ }
+ rowkeep <- unique(rowkeep)
+ rowkeep
+}
+
#from summary.ca
summary.ca.dm <- function(object, scree = TRUE, ...){
obj <- object
res
}
-make_afc_graph <- function(toplot,classes,clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE) {
- rain <- rainbow(clnb)
+is.yellow <- function(my.color) {
+ if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
+ return(TRUE)
+ } else {
+ return(FALSE)
+ }
+}
+
+del.yellow <- function(colors) {
+ rgbs <- col2rgb(colors)
+ tochange <- apply(rgbs, 2, is.yellow)
+ tochange <- which(tochange)
+ if (length(tochange)) {
+ gr.col <- grey.colors(length(tochange), start = 0.5, end = 0.8)
+ }
compt <- 1
- tochange <- NULL
- for (my.color in rain) {
- my.color <- col2rgb(my.color)
- if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
- tochange <- append(tochange, compt)
- }
+ for (val in tochange) {
+ colors[val] <- gr.col[compt]
compt <- compt + 1
}
- if (!is.null(tochange)) {
- gr.col <- grey.colors(length(tochange))
- compt <- 1
- for (val in tochange) {
- rain[val] <- gr.col[compt]
- compt <- compt + 1
- }
+ colors
+}
+
+make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL, color=NULL) {
+
+ rain <- rainbow(clnb)
+ compt <- 1
+ tochange <- NULL
+ #for (my.color in rain) {
+ # my.color <- col2rgb(my.color)
+ # if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
+ # tochange <- append(tochange, compt)
+ # }
+ # compt <- compt + 1
+ #}
+ #if (!is.null(tochange)) {
+ # gr.col <- grey.colors(length(tochange))
+ # compt <- 1
+ # for (val in tochange) {
+ # rain[val] <- gr.col[compt]
+ # compt <- compt + 1
+ # }
+ #}
+ rain <- del.yellow(rain)
+ cl.color <- rain[classes]
+ if (black) {
+ cl.color <- 'black'
+ }
+ if (!is.null(color)) {
+ cl.color <- color
}
- cl.color <- rain[classes]
- plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab)
- abline(h=0,v=0, lty = 'dashed')
+ plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab, xlim=xminmax, ylim = yminmax)
+ abline(h=0, v=0, lty = 'dashed')
if (is.null(cex.txt))
- text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color)
+ text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, offset=0)
else
- text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt)
+ #require(wordcloud)
+ #textplot(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt, xlim=xminmax, ylim = yminmax)
+ text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt, offset=0)
if (!cmd) {
dev.off()
}
}
+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$tip.label)
+ vec.mat<-NULL
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ #et.keep <- select.chi.classe.et(chisqtable, 10)
+ #print(chistable[et.keep,])
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ names(ntoplot) <- rownames(toplot)
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ if (length(toplot) > nbbycl) {
+ ntoplot <- ntoplot[1:nbbycl]
+ }
+ ntoplot <- ntoplot[which(ntoplot > 0)]
+ #ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ vec.mat <- matrix(1, nrow = 3, ncol = length(sum.cl))
+ vec.mat[2,] <- 2
+ vec.mat[3,] <- 3:(length(sum.cl)+2)
+ layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(2,1,6))
+ if (! bw) {
+ col <- rainbow(length(sum.cl))
+ col <- del.yellow(col)
+ col <- col[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ colcloud <- del.yellow(colcloud)
+ }
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ par(mar=c(2,1,0,1))
+ plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, y.lim=c(-0.3,tree$Nnode))
+ par(mar=c(0,0,0,0))
+ d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)
+ text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1)
+ 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]], 2, 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)
+ }
+ }
+ if (!from.cmd) {
+ dev.off()
+ }
+
+}
+
+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$tip.label)
+ vec.mat<-NULL
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ names(ntoplot) <- rownames(toplot)
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ if (length(toplot) > nbbycl) {
+ ntoplot <- ntoplot[1:nbbycl]
+ }
+ ntoplot <- ntoplot[order(ntoplot)]
+ ntoplot <- ntoplot[which(ntoplot > 0)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1)
+ v<-2
+ for (i in 1:length(sum.cl)) {
+ vec.mat<-append(vec.mat,v)
+ v<-v+1
+ }
+ layout(matrix(vec.mat,length(sum.cl),2),widths=c(1,2))
+ if (! bw) {
+ col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ }
+ par(mar=c(0,0,0,0))
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(2.5, 0.5), random.order=FALSE, colors = colcloud[i])
+ }
+}
+
plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) {
classes<-classes[classes!=0]
classes<-as.factor(classes)
- sum.cl<-as.matrix(summary(classes))
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
sum.cl<-(sum.cl/colSums(sum.cl)*100)
sum.cl<-round(sum.cl,2)
sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
tree.order<- as.numeric(tree$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 <- del.yellow(col)
col.bars <- col
col.pie <- rainbow(nrow(sum.cl))
+ col.pie <- del.yellow(col.pie)
#col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
} else {
col = 'black'
}
}
par(mar=c(0,0,0,0),cex=1)
- label.ori<-tree[[2]]
+ label.ori<-tree$tip.label
if (!is.null(lab)) {
tree$tip.label <- lab
} else {
- tree[[2]]<-paste('classe ',tree[[2]])
+ tree$tip.label<-paste('classe ',tree$tip.label)
}
plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
#cl.order <- as.numeric(label.ori)
}
#tree <- tree.cut1$tree.cl
#to.plot <- di
-plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), cmd=FALSE) {
+plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, direction = 'rightwards', cmd=FALSE) {
tree.order<- as.numeric(tree$tip.label)
+ if (!is.null(classes)) {
+ 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]))
+ }
par(mar=c(0,0,0,0))
- layout(matrix(c(1,2,3),1,byrow=TRUE), widths=lay.width,TRUE)
- par(mar=c(3,0,2,0),cex=1)
+ if (direction == 'rightwards') {
+ srt <- 0
+ adj <- NULL
+ horiz <- TRUE
+ if (!is.null(classes)) {
+ matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
+ lay.width <- c(3,2,3,2)
+ } else {
+ matlay <- matrix(c(1,2,3),1,byrow=TRUE)
+ }
+ } else {
+ srt <- 90
+ adj <- 0.5
+ horiz <- FALSE
+ if (!is.null(classes)) {
+ matlay <- matrix(c(1,2,3,4,4,4),3)
+ } else {
+ matlay <- matrix(c(1,2,3,3),2)
+ }
+ lay.width <- c(5,2)
+ }
+ layout(matlay, widths=lay.width,TRUE)
+ par(mar=c(3,0,2,4),cex=1)
label.ori<-tree[[2]]
if (!is.null(lab)) {
- tree$tip.label <- lab
+ tree$tip.label <- lab[tree.order]
} else {
tree[[2]]<-paste('classe ',tree[[2]])
}
to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
if (!bw) {
- col <- rainbow(ncol(to.plot))
- col.bars <- rainbow(nrow(to.plot))
+ col <- rainbow(ncol(to.plot))
+ col <- del.yellow(col)
+ if (is.null(colbar)) {
+ col.bars <- rainbow(nrow(to.plot))
+ col.bars <- del.yellow(col.bars)
+ } else {
+ col.bars <- colbar
+ }
} else {
col <- 'black'
col.bars <- grey.colors(nrow(to.plot),0,0.8)
}
col <- col[tree.order]
- plot.phylo(tree,label.offset=0.1,tip.col=col)
-
+ plot.phylo(tree,label.offset=0.2,tip.col=col, direction = direction, srt=srt, adj = 0.5, edge.width = 2)
+ if (!is.null(classes)) {
+ par(cex=0.7)
+ par(mar=c(3,0,2,1))
+ to.plota <- sum.cl[tree.order,1]
+ d <- barplot(to.plota,horiz=TRUE, col=col, names.arg='', axes=FALSE, axisname=FALSE)
+ text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2)
+ }
par(mar=c(3,0,2,1))
- d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
+ d <- barplot(to.plot,horiz=horiz, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
c <- colMeans(d)
c1 <- c[-1]
c2 <- c[-length(c)]
}
par(mar=c(0,0,0,0))
plot(0, axes = FALSE, pch = '')
- legend(x = 'center' , rownames(to.plot), fill = col.bars)
+ legend(x = 'center' , rev(rownames(to.plot)), fill = rev(col.bars))
if (!cmd) {
dev.off()
}
cc<-mc[cc]
#mass<-(rowSums(x)/max(rowSums(x))) * 5
maxchi<-norm.vec(maxchi, 0.03, 0.3)
- rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color='black',vertex.color=cc,vertex.size = 0.1, layout=lo, rescale=FALSE)
- rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
+ rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color= cc,vertex.label.cex = maxchi, vertex.size = 0.1, layout=lo, rescale=FALSE)
+ text3d(lo[,1], lo[,2],lo[,3], rownames(x), cex=maxchi, col=cc)
+ #rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
rgl.bg(color = c('white','black'))
if (!is.null(movie)) {
require(tcltk)
#d <- barplot(to.plot,horiz=TRUE, names.arg='', axes=FALSE, axisname=FALSE)
#text(x=to.plot, y=d[,1], label=round(to.plot,1), adj=1.2)
+make.afc.attributes <- function(rn, afc.table, contafc, clnb, column = FALSE, x=1, y=2) {
+ if (!column){
+ nd <- clnb - 1
+ afc.res <- afc.table$ligne
+ #tokeep <- which(row.names(afc.res) %in% rn)
+ afc.res <- afc.res[rn,]
+ debcor <- (nd*2) + 1
+ cor <- afc.res[,debcor:(debcor+nd-1)][,c(x,y)]
+ debctr <- (nd*3) + 1
+ ctr <- afc.res[,debctr:(debctr+nd-1)][,c(x,y)]
+ massdeb <- (nd*4) + 1
+ mass <- afc.res[,massdeb]
+ chideb <- massdeb + 1
+ chi <- afc.res[,chideb]
+ inertiadeb <- chideb + 1
+ inertia <- afc.res[,inertiadeb]
+ frequence <- rowSums(contafc[rn,])
+ }
+ res <- list(frequence=frequence, cor, ctr, mass = mass, chi=chi, inertia=inertia)
+ return(res)
+}
+
+
+afctogexf <- function(fileout, toplot, classes, clnb, sizes, nodes.attr=NULL) {
+ toplot <- toplot[,1:3]
+ toplot[,3] <- 0
+ #toplot <- afc$rowcoord[1:100,1:3]
+ #toplot[,3] <- 0
+ #rownames(toplot)<-afc$rownames[1:100]
+ cc <- rainbow(clnb)[classes]
+ cc <- t(sapply(cc, col2rgb, alpha=TRUE))
+ #sizes <- apply(chistabletot[1:100,], 1, max)
+
+ nodes <- data.frame(cbind(1:nrow(toplot), rownames(toplot)))
+ colnames(nodes) <- c('id', 'label')
+ nodes[,1] <- as.character(nodes[,1])
+ nodes[,2] <- as.character(nodes[,2])
+ #nodes attributs
+ if (! is.null(nodes.attr)) {
+ nodesatt <- as.data.frame(nodes.attr)
+ } else {
+ nodesatt <- data.frame(cbind(toplot[,1],toplot[,2]))
+ }
+ #make axes
+ edges<-matrix(c(1,1),ncol=2)
+ xmin <- min(toplot[,1])
+ xmax <- max(toplot[,1])
+ ymin <- min(toplot[,2])
+ ymax <- max(toplot[,2])
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
+ nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ nodesatt<-rbind(nodesatt, c(0,0))
+ toplot <- rbind(toplot, c(xmin, 0,0))
+ toplot <- rbind(toplot, c(xmax,0,0))
+ toplot <- rbind(toplot, c(0,ymin,0))
+ toplot <- rbind(toplot, c(0,ymax,0))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ cc <- rbind(cc, c(255,255,255,1))
+ sizes <- c(sizes, c(0.5, 0.5, 0.5, 0.5))
+ edges <- rbind(edges, c(nrow(nodes)-3, nrow(nodes)-2))
+ edges <- rbind(edges, c(nrow(nodes)-1, nrow(nodes)))
+ write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=cc, position=toplot, size=sizes))
+}
+
+simi.to.gexf <- function(fileout, graph.simi, nodes.attr = NULL) {
+ lo <- graph.simi$layout
+ if (ncol(lo) == 3) {
+ lo[,3] <- 0
+ } else {
+ lo <- cbind(lo, rep(0,nrow(lo)))
+ }
+ g <- graph.simi$graph
+ nodes <- data.frame(cbind(1:nrow(lo), V(g)$name))
+ colnames(nodes) <- c('id', 'label')
+ if (! is.null(nodes.attr)) {
+ nodesatt <- as.data.frame(nodes.attr)
+ } else {
+ nodesatt <- data.frame(cbind(lo[,1],lo[,2]))
+ }
+ edges <- as.data.frame(get.edges(g, c(1:ecount(g))))
+ col <- graph.simi$color
+ col <- t(sapply(col, col2rgb, alpha=TRUE))
+ write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo, size=graph.simi$label.cex), edgesVizAtt=list(size=graph.simi$we.width))
+}
+
+graphml.to.file <- function(graph.path) {
+ library(igraph)
+ g <- read.graph(graph.path, format='graphml')
+ layout <- layout.fruchterman.reingold(g, dim=3)
+ #print(V(g)$color)
+ graph.simi <- list(graph=g, layout=layout, color = V(g)$color ,eff=V(g)$weight)
+ graph.simi
+}
+
+
+
+graph.to.file <- function(graph.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+ require(igraph)
+ g <- graph.simi$graph
+ print(graph.simi$eff)
+ if (!is.null(graph.simi$eff)) {
+ V(g)$weight <- graph.simi$eff
+ } else {
+ V(g)$weight <- graph.simi$label.cex
+ }
+ layout <- layout.norm(graph.simi$layout,-5,5,-5,5,-5,5)
+ print(layout)
+ V(g)$x <- layout[,1]
+ V(g)$y <- layout[,2]
+ if (ncol(layout) == 3) {
+ V(g)$z <- layout[,3]
+ }
+ if (community) {
+ member <- graph.simi$communities$membership
+ col <- rainbow(max(member))
+ v.colors <- col[member]
+ v.colors <- col2rgb(v.colors)
+ V(g)$r <- v.colors[1,]
+ V(g)$g <- v.colors[2,]
+ V(g)$b <- v.colors[3,]
+ }
+ if (!is.null(color)) {
+ v.colors <- col2rgb(color)
+ V(g)$r <- v.colors[1,]
+ V(g)$g <- v.colors[2,]
+ V(g)$b <- v.colors[3,]
+ }
+ if (!is.null(sweight)) {
+ V(g)$sweight <- sweight
+ }
+ df <- get.data.frame(g, what='both')
+ if (!is.null(nodesfile)) {
+ write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)
+ }
+ if (!is.null(edgesfile)) {
+ write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
+ }
+ if (is.null(edgesfile) & is.null(nodesfile)) {
+ df
+ }
+}
+
+graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+ require(igraph)
+ g <- graph
+ V(g)$x <- layout[,1]
+ V(g)$y <- layout[,2]
+ if (ncol(layout) == 3) {
+ V(g)$z <- layout[,3]
+ }
+ v.colors <- col2rgb(V(g)$color)
+ V(g)$r <- v.colors[1,]
+ V(g)$g <- v.colors[2,]
+ V(g)$b <- v.colors[3,]
+
+ if (!is.null(sweight)) {
+ V(g)$sweight <- sweight
+ }
+ if (is.null(V(g)$weight)) {
+ if (!is.null(sweight)) {
+ V(g)$weight <- sweight
+ } else {
+ V(g)$weight <- 1
+ }
+ }
+ df <- get.data.frame(g, what='both')
+ if (!is.null(nodesfile)) {
+ write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)
+ }
+ if (!is.null(edgesfile)) {
+ write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
+ }
+ if (is.null(edgesfile) & is.null(nodesfile)) {
+ df
+ }
+}
+
projects / iramuteq / blobdiff