1 ############FIXME##################
2 #PlotDendroComp <- function(chd,filename,reso) {
3 # jpeg(filename,res=reso)
5 # plot(chd,which.plots=2, hang=-1)
9 #PlotDendroHori <- function(dendrocutupper,filename,reso) {
10 # jpeg(filename,res=reso)
12 # 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')
13 # plot(dendrocutupper,nodePar= nP, edgePar = list(col='gray', lwd=2),horiz=TRUE, center=FALSE)
17 PlotDendroCut <- function(chd,filename,reso,clusternb) {
18 h.chd <- as.hclust(chd)
19 memb <- cutree(h.chd, k = clusternb)
21 for(k in 1:clusternb){
22 cent <- rbind(cent, k)
24 h.chd1 <- hclust(dist(cent)^2, method = 'cen', members = table(memb))
25 h.chd1$labels <- sprintf('CL %02d',1:clusternb)
26 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
27 jpeg(filename,res=reso)
29 plot(h.chd1, nodePar= nP, edgePar = list(col='gray', lwd=2), horiz=TRUE, center=TRUE, hang= -1)
33 #PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
34 # if (Sys.info()["sysname"]=='Darwin') {
36 # height<-height/74.97
37 # quartz(file=filename,type='jpeg',width=width,height=height)
39 # jpeg(filename,width=width,height=height,quality=quality,res=reso)
42 # plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
46 PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL, active = TRUE) {
48 if (what == 'coord') {
49 rowcoord <- as.matrix(afc$colcoord)
51 rowcoord <- as.matrix(afc$colcrl)
54 if (what == 'coord') {
55 rowcoord <- as.matrix(afc$rowcoord)
57 rowcoord <- as.matrix(afc$rowcrl)
63 rownames(rowcoord) <- afc$colnames
65 rownames(rowcoord) <- afc$rownames
66 rowcoord <- as.matrix(rowcoord[deb:fin,])
67 chitable<- as.matrix(chisqrtable[deb:fin,])
68 #row_keep <- select_point_nb(chitable,15)
70 if (ncol(rowcoord) == 1) {
71 rowcoord <- t(rowcoord)
73 clnb <- ncol(chisqrtable)
76 classes <- as.matrix(apply(chitable,1,which.max))
77 cex.par <- norm.vec(apply(chitable,1,max), 0.8,3)
78 row.keep <- select.chi.classe(chitable, 80, active=active)
79 rowcoord <- rowcoord[row.keep,]
80 classes <- classes[row.keep]
81 cex.par <- cex.par[row.keep]
84 cex.par <- rep(1,clnb)
88 xminmax <- c(min(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,1], na.rm = TRUE)), max(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,1], na.rm = TRUE)))
91 yminmax <- c(min(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,2], na.rm = TRUE)), max(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,2], na.rm = TRUE)))
95 #ntabtot <- cbind(rowcoord, classes)
96 #if (!col) ntabtot <- ntabtot[row_keep,]
97 xlab <- paste('facteur ', x, ' -')
98 ylab <- paste('facteur ', y, ' -')
99 xlab <- paste(xlab,round(afc_table$facteur[x,2],2),sep = ' ')
100 xlab <- paste(xlab,' %%',sep = '')
101 ylab <- paste(ylab,round(afc_table$facteur[y,2],2),sep = ' ')
102 ylab <- paste(ylab,' %%',sep = '')
104 open_file_graph(filename, width = width, height = height)
106 table.in <- rowcoord[order(cex.par, decreasing = TRUE),]
107 classes <- classes[order(cex.par, decreasing = TRUE)]
108 cex.par <- cex.par[order(cex.par, decreasing = TRUE)]
109 table.out <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax))
110 table.in <- table.out$toplot
111 notplot <- table.out$notplot
112 if (! is.null(notplot)) {
113 write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = ''))
115 classes <- classes[table.in[,4]]
116 cex.par <- cex.par[table.in[,4]]
117 make_afc_graph(table.in, classes, clnb, xlab, ylab, cex.txt = cex.par, xminmax=c(xmin,xmax), yminmax=c(ymin,ymax))
118 xyminmax <- list(yminmax = c(ymin,ymax), xminmax = c(xmin,xmax))
120 #plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
123 # ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
124 # if (nrow(ntab) != 0)
125 # text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
130 filename.to.svg <- function(filename) {
131 filename <- gsub('.png', '.svg', filename)
135 open_file_graph <- function (filename, width=800, height = 800, quality = 100, svg = FALSE) {
136 if (Sys.info()["sysname"] == 'Darwin') {
138 height <- height/74.97
140 quartz(file = filename, type = 'png', width = width, height = height)
142 svg(filename.to.svg(filename), width=width, height=height)
146 svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
148 png(filename, width=width, height=height)#, quality = quality)
153 #################################################@@
155 overlap <- function(x1, y1, sw1, sh1, boxes) {
156 use.r.layout <- FALSE
158 return(.overlap(x1,y1,sw1,sh1,boxes))
160 if (length(boxes) == 0)
162 for (i in c(last,1:length(boxes))) {
169 overlap <- x1 + sw1 > x2-s
171 overlap <- x2 + sw2 > x1-s
174 overlap <- overlap && (y1 + sh1 > y2-s)
176 overlap <- overlap && (y2 + sh2 > y1-s)
185 .overlap <- function(x11,y11,sw11,sh11,boxes1){
186 .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
188 ########################################################
189 stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
201 plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim)
204 if (is.null(cex.par)) {
205 size <- rep(0.9, nrow(x))
209 #cols <- rainbow(clnb)
211 for (i in 1:nrow(x)) {
212 rotWord <- runif(1)<rot.per
214 theta <- runif(1,0,2*pi)
217 wid <- strwidth(words[i],cex=size[i])
218 ht <- strheight(words[i],cex=size[i])
221 if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
222 toplot <- rbind(toplot, c(x1, y1, size[i], i))
223 #text(x1,y1,words[i],cex=size[i],offset=0,srt=rotWord*90,
224 # col=cols[classes[i]])
225 boxes[[length(boxes)+1]] <- c(x1-.5*wid,y1-.5*ht,wid,ht)
229 print(paste(words[i], "could not be fit on page. It will not be plotted."))
230 notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2]))
233 theta <- theta+thetaStep
234 r <- r + rStep*thetaStep/(2*pi)
235 x1 <- x[i,1]+r*cos(theta)
236 y1 <- x[i,2]+r*sin(theta)
240 row.names(toplot) <- words[toplot[,4]]
241 return(list(toplot = toplot, notplot = notplot))
243 ###############################################################################
245 make_tree_tot <- function (chd) {
249 for (i in 1:length(lf)) {
250 if (!is.null(lf[[i]])) {
251 clus<-gsub(paste('a',i,'a',sep=''),paste('(','a',lf[[i]][1],'a',',','a',lf[[i]][2],'a',')',sep=''),clus)
255 clus <- gsub('a','',clus)
256 tree.cl <- read.tree(text = clus)
257 res<-list(tree.cl = tree.cl, dendro_tuple = dendro_tuple)
261 make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) {
265 for (cl in coordok[,x]) {
267 fcl<-fille(cl,classeuce)
269 dendro <- gsub(paste('a',fi,'a',sep=''),paste('b',i,'b',sep=''),dendro)
272 clnb <- nrow(coordok)
274 for (i in 1:(tcl + 1)) {
275 dendro <- gsub(paste('a',i,'a',sep=''),paste('b',0,'b',sep=''),dendro)
277 dendro <- gsub('b','',dendro)
278 dendro <- gsub('a','',dendro)
279 dendro_tot_cl <- read.tree(text = dendro)
283 dendro <- gsub(paste('\\(',cl,',',cl,'\\)',sep=''),cl,dendro)
287 dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro)
289 dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro)
290 dendro <- gsub(paste('\\(',cl,',',0,'\\)',sep=''),cl,dendro)
294 tree.cl <- read.tree(text = dendro)
295 lab <- tree.cl$tip.label
297 tovire <- which(lab == "0")
298 tree.cl <- drop.tip(tree.cl, tip = tovire)
300 res <- list(tree.cl = tree.cl, dendro_tuple_cut = dendro, dendro_tot_cl = dendro_tot_cl)
304 select_point_nb <- function(tablechi, nb) {
305 chimax<-as.matrix(apply(tablechi,1,max))
306 chimax<-cbind(chimax,1:nrow(tablechi))
307 order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),])
308 row_keep <- order_chi[,2][1:nb]
312 select_point_chi <- function(tablechi, chi_limit) {
313 chimax<-as.matrix(apply(tablechi,1,max))
314 row_keep <- which(chimax >= chi_limit)
318 select.chi.classe <- function(tablechi, nb, active = TRUE) {
320 if (active & !is.null(debsup)) {
322 print('###############################################################@')
323 tablechi <- tablechi[1:(debsup-1),]
325 if (nb > nrow(tablechi)) {
328 for (i in 1:ncol(tablechi)) {
329 rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
331 rowkeep <- unique(rowkeep)
336 summary.ca.dm <- function(object, scree = TRUE, ...){
342 if (nd > length(obj$sv)) nd <- length(obj$sv)
344 # principal coordinates:
346 I <- dim(obj$rowcoord)[1] ; J <- dim(obj$colcoord)[1]
347 svF <- matrix(rep(obj$sv[1:K], I), I, K, byrow = TRUE)
348 svG <- matrix(rep(obj$sv[1:K], J), J, K, byrow = TRUE)
349 rpc <- obj$rowcoord[,1:K] * svF
350 cpc <- obj$colcoord[,1:K] * svG
353 r.names <- obj$rownames
355 if (!is.na(sr[1])) r.names[sr] <- paste("(*)", r.names[sr], sep = "")
356 r.mass <- obj$rowmass
357 r.inr <- obj$rowinertia / sum(obj$rowinertia, na.rm = TRUE)
358 r.COR <- matrix(NA, nrow = length(r.names), ncol = nd)
359 colnames(r.COR) <- paste('COR -facteur', 1:nd, sep=' ')
360 r.CTR <- matrix(NA, nrow = length(r.names), ncol = nd)
361 colnames(r.CTR) <- paste('CTR -facteur', 1:nd, sep=' ')
363 r.COR[,i] <- obj$rowmass * rpc[,i]^2 / obj$rowinertia
364 r.CTR[,i] <- obj$rowmass * rpc[,i]^2 / obj$sv[i]^2
366 # cor and quality for supplementary rows
367 if (length(obj$rowsup) > 0){
370 r.COR[i0,i] <- obj$rowmass[i0] * rpc[i0,i]^2
376 c.names <- obj$colnames
378 if (!is.na(sc[1])) c.names[sc] <- paste("(*)", c.names[sc], sep = "")
379 c.mass <- obj$colmass
380 c.inr <- obj$colinertia / sum(obj$colinertia, na.rm = TRUE)
381 c.COR <- matrix(NA, nrow = length(c.names), ncol = nd)
382 colnames(c.COR) <- paste('COR -facteur', 1:nd, sep=' ')
383 c.CTR <- matrix(NA, nrow = length(c.names), ncol = nd)
384 colnames(c.CTR) <- paste('CTR -facteur', 1:nd, sep=' ')
387 c.COR[,i] <- obj$colmass * cpc[,i]^2 / obj$colinertia
388 c.CTR[,i] <- obj$colmass * cpc[,i]^2 / obj$sv[i]^2
390 if (length(obj$colsup) > 0){
393 c.COR[i0,i] <- obj$colmass[i0] * cpc[i0,i]^2
401 values2 <- 100*(obj$sv^2)/sum(obj$sv^2)
402 values3 <- cumsum(100*(obj$sv^2)/sum(obj$sv^2))
403 scree.out <- cbind(values, values2, values3)
412 obj$facteur <- scree.out
416 create_afc_table <- function(x) {
418 facteur.table <- as.matrix(x$facteur)
419 nd <- ncol(x$colcoord)
420 rownames(facteur.table) <- paste('facteur',1:nrow(facteur.table),sep = ' ')
421 colnames(facteur.table) <- c('Valeurs propres', 'Pourcentages', 'Pourcentage cumules')
422 ligne.table <- as.matrix(x$rowcoord)
423 rownames(ligne.table) <- x$rownames
424 colnames(ligne.table) <- paste('Coord. facteur', 1:nd, sep=' ')
425 tmp <- as.matrix(x$rowcrl)
426 colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ')
427 ligne.table <- cbind(ligne.table,tmp)
428 ligne.table <- cbind(ligne.table, x$r.COR)
429 ligne.table <- cbind(ligne.table, x$r.CTR)
430 ligne.table <- cbind(ligne.table, mass = x$rowmass)
431 ligne.table <- cbind(ligne.table, chi.distance = x$rowdist)
432 ligne.table <- cbind(ligne.table, inertie = x$rowinertia)
433 colonne.table <- x$colcoord
434 rownames(colonne.table) <- paste('classe', 1:(nrow(colonne.table)),sep=' ')
435 colnames(colonne.table) <- paste('Coord. facteur', 1:nd, sep=' ')
436 tmp <- as.matrix(x$colcrl)
437 colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ')
438 colonne.table <- cbind(colonne.table, tmp)
439 colonne.table <- cbind(colonne.table, x$c.COR)
440 colonne.table <- cbind(colonne.table, x$c.CTR)
441 colonne.table <- cbind(colonne.table, mass = x$colmass)
442 colonne.table <- cbind(colonne.table, chi.distance = x$coldist)
443 colonne.table <- cbind(colonne.table, inertie = x$colinertia)
444 res <- list(facteur = facteur.table, ligne = ligne.table, colonne = colonne.table)
448 is.yellow <- function(my.color) {
449 if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
456 del.yellow <- function(colors) {
457 rgbs <- col2rgb(colors)
458 tochange <- apply(rgbs, 2, is.yellow)
459 tochange <- which(tochange)
460 if (length(tochange)) {
461 gr.col <- grey.colors(length(tochange))
464 for (val in tochange) {
465 colors[val] <- gr.col[compt]
471 make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
473 rain <- rainbow(clnb)
476 for (my.color in rain) {
477 my.color <- col2rgb(my.color)
478 if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
479 tochange <- append(tochange, compt)
483 if (!is.null(tochange)) {
484 gr.col <- grey.colors(length(tochange))
486 for (val in tochange) {
487 rain[val] <- gr.col[compt]
491 cl.color <- rain[classes]
495 plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab, xlim=xminmax, ylim = yminmax)
496 abline(h=0, v=0, lty = 'dashed')
497 if (is.null(cex.txt))
498 text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, offset=0)
500 text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt, offset=0)
507 plot.dendro.prof <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) {
510 classes<-classes[classes!=0]
511 classes<-as.factor(classes)
512 sum.cl<-as.matrix(summary(classes, maxsum=1000000))
513 sum.cl<-(sum.cl/colSums(sum.cl)*100)
514 sum.cl<-round(sum.cl,2)
515 sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
517 tree.order<- as.numeric(tree$tip.label)
519 row.keep <- select.chi.classe(chisqtable, nbbycl)
520 toplot <- chisqtable[row.keep,]
522 for (classe in 1:length(sum.cl)) {
523 ntoplot <- toplot[,classe]
524 names(ntoplot) <- rownames(toplot)
525 ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
526 ntoplot <- round(ntoplot, 0)
527 ntoplot <- ntoplot[1:nbbycl]
528 #ntoplot <- ntoplot[order(ntoplot)]
529 #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
530 lclasses[[classe]] <- ntoplot
532 vec.mat <- matrix(1, nrow = 3, ncol = length(sum.cl))
534 vec.mat[3,] <- 3:(length(sum.cl)+2)
535 layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(1,1,6))
537 col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
538 col <- del.yellow(col)
539 colcloud <- rainbow(length(sum.cl))
540 colcloud <- del.yellow(colcloud)
544 tree$tip.label <- lab
546 tree[[2]]<-paste('classe ',tree[[2]])
549 plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
551 d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)
552 text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1.4)
553 for (i in tree.order) {
554 par(mar=c(0,0,1,0),cex=0.7)
555 #wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(1.5, 0.2), random.order=FALSE, colors = colcloud[i])
557 plot(0,0,pch='', axes = FALSE)
558 vcex <- norm.vec(lclasses[[i]], 1.5, 2.5)
559 for (j in 1:length(lclasses[[i]])) {
560 yval <- yval-(strheight( names(lclasses[[i]])[j],cex=vcex[j])+0.02)
561 text(-0.9, yval, names(lclasses[[i]])[j], cex = vcex[j], col = colcloud[i], adj=0)
567 plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", from.cmd = FALSE, bw = FALSE, lab = NULL) {
570 classes<-classes[classes!=0]
571 classes<-as.factor(classes)
572 sum.cl<-as.matrix(summary(classes, maxsum=1000000))
573 sum.cl<-(sum.cl/colSums(sum.cl)*100)
574 sum.cl<-round(sum.cl,2)
575 sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
577 tree.order<- as.numeric(tree$tip.label)
579 row.keep <- select.chi.classe(chisqtable, nbbycl)
580 toplot <- chisqtable[row.keep,]
582 for (classe in 1:length(sum.cl)) {
583 ntoplot <- toplot[,classe]
584 ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
585 ntoplot <- round(ntoplot, 0)
586 ntoplot <- ntoplot[1:nbbycl]
587 ntoplot <- ntoplot[order(ntoplot)]
588 #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
589 lclasses[[classe]] <- ntoplot
591 for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1)
593 for (i in 1:length(sum.cl)) {
594 vec.mat<-append(vec.mat,v)
597 layout(matrix(vec.mat,length(sum.cl),2),widths=c(1,2))
599 col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
600 colcloud <- rainbow(length(sum.cl))
605 tree$tip.label <- lab
607 tree[[2]]<-paste('classe ',tree[[2]])
609 plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
610 for (i in rev(tree.order)) {
611 par(mar=c(0,0,1,0),cex=0.9)
612 wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(4, 0.8), random.order=FALSE, colors = colcloud[i])
616 plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) {
617 classes<-classes[classes!=0]
618 classes<-as.factor(classes)
619 sum.cl<-as.matrix(summary(classes, maxsum=1000000))
620 sum.cl<-(sum.cl/colSums(sum.cl)*100)
621 sum.cl<-round(sum.cl,2)
622 sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
623 tree.order<- as.numeric(tree$tip.label)
627 col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)]
628 col <- del.yellow(col)
630 col.pie <- rainbow(nrow(sum.cl))
631 col.pie <- del.yellow(col.pie)
632 #col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
636 col.pie <- rep('grey',nrow(sum.cl))
639 for (i in 1:nrow(sum.cl)) vec.mat<-append(vec.mat,1)
641 for (i in 1:nrow(sum.cl)) {
642 vec.mat<-append(vec.mat,v)
648 layout(matrix(vec.mat,nrow(sum.cl),2),widths=c(3,1))
650 layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE)
653 par(mar=c(0,0,0,0),cex=1)
656 tree$tip.label <- lab
658 tree[[2]]<-paste('classe ',tree[[2]])
660 plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
661 #cl.order <- as.numeric(label.ori)
663 #for (i in 1:nrow(sum.cl)) {
666 for (i in rev(tree.order)) {
667 par(mar=c(0,0,1,0),cex=0.7)
668 pie(sum.cl[i,],col=c(col.pie[i],'white'),radius = 1, labels='', clockwise=TRUE, main = paste('classe ',i,' - ',sum.cl[i,1],'%' ))
673 to.plot <- sum.cl[tree.order,1]
674 d <- barplot(to.plot,horiz=TRUE, col=col.bars, names.arg='', axes=FALSE, axisname=FALSE)
675 text(x=to.plot, y=d[,1], label=paste(round(to.plot,1),'%'), adj=1.2)
678 if (!from.cmd) dev.off()
681 #tree <- tree.cut1$tree.cl
683 plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, cmd=FALSE) {
684 tree.order<- as.numeric(tree$tip.label)
685 if (!is.null(classes)) {
686 classes<-classes[classes!=0]
687 classes<-as.factor(classes)
688 sum.cl<-as.matrix(summary(classes, maxsum=1000000))
689 sum.cl<-(sum.cl/colSums(sum.cl)*100)
690 sum.cl<-round(sum.cl,2)
691 sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
694 if (!is.null(classes)) {
695 matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
696 lay.width <- c(3,1,3,2)
698 matlay <- matrix(c(1,2,3),1,byrow=TRUE)
700 layout(matlay, widths=lay.width,TRUE)
701 par(mar=c(3,0,2,0),cex=1)
704 tree$tip.label <- lab
706 tree[[2]]<-paste('classe ',tree[[2]])
708 to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
710 col <- rainbow(ncol(to.plot))
711 col <- del.yellow(col)
712 if (is.null(colbar)) {
713 col.bars <- rainbow(nrow(to.plot))
714 col.bars <- del.yellow(col.bars)
720 col.bars <- grey.colors(nrow(to.plot),0,0.8)
722 col <- col[tree.order]
723 plot.phylo(tree,label.offset=0.1,tip.col=col)
724 if (!is.null(classes)) {
727 to.plota <- sum.cl[tree.order,1]
728 d <- barplot(to.plota,horiz=TRUE, col=col, names.arg='', axes=FALSE, axisname=FALSE)
729 text(x=to.plota, y=d[,1], label=paste(round(to.plota,1),'%'), adj=1.2)
732 d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
737 lcoord <- apply(cc, 1, mean)
739 if (min(to.plot) < 0) {
740 amp <- abs(max(to.plot) - min(to.plot))
747 d <- signif(amp%/%10,1)
749 mn <- round(min(to.plot))
750 mx <- round(max(to.plot))
752 if ((i/d) == (i%/%d)) {
757 plot(0, axes = FALSE, pch = '')
758 legend(x = 'center' , rownames(to.plot), fill = col.bars)
765 plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) {
767 if (is.null(debsup)) {
768 tab.toplot<-afctable[1:(debet+1),]
769 chitab<-chistabletot[1:(debet+1),]
771 tab.toplot<-afctable[1:(debsup+1),]
772 chitab<-chistabletot[1:(debsup+1),]
774 rkeep<-select_point_chi(chitab,chilim)
775 tab.toplot<-tab.toplot[rkeep,]
776 chitab<-chitab[rkeep,]
777 dm<-dist(tab.toplot,diag=TRUE,upper=TRUE)
778 cn<-rownames(tab.toplot)
779 cl.toplot<-apply(chitab,1,which.max)
780 col<-rainbow(ncol(tab.toplot))[cl.toplot]
782 g1 <- graph.adjacency(as.matrix(dm), mode = 'lower', weighted = TRUE)
783 g.max<-minimum.spanning.tree(g1)
784 we<-(rowSums(tab.toplot)/max(rowSums(tab.toplot)))*2
785 #lo <- layout.fruchterman.reingold(g.max,dim=nd)
786 lo<- layout.kamada.kawai(g.max,dim=nd)
787 print(nrow(tab.toplot))
793 rglplot(g.max, vertex.label = cn, vertex.size = we*3, edge.width = 0.5, edge.color='black', vertex.label.color = col,vertex.color = col, layout = lo, vertex.label.cex = 1)
794 } else if (nd == 2) {
795 plot(g.max, vertex.label = cn, vertex.size = we, edge.width = 0.5, edge.color='black', vertex.label.color = col,vertex.color = col, layout = lo, vertex.label.cex = 0.8)
800 make.simi.afc <- function(x,chitable,lim=0, alpha = 0.1, movie = NULL) {
802 chimax<-as.matrix(apply(chitable,1,max))
803 chimax<-as.matrix(chimax[,1][1:nrow(x)])
804 chimax<-cbind(chimax,1:nrow(x))
805 order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),])
806 if ((lim == 0) || (lim>nrow(x))) lim <- nrow(x)
807 x<-x[order_chi[,2][1:lim],]
808 maxchi <- chimax[order_chi[,2][1:lim],1]
809 #-------------------------------------------------------
811 distm<-dist(x,diag=TRUE)
812 distm<-as.matrix(distm)
813 g1<-graph.adjacency(distm,mode='lower',weighted=TRUE)
814 g1<-minimum.spanning.tree(g1)
815 lo<-layout.kamada.kawai(g1,dim=3)
816 lo <- layout.norm(lo, -3, 3, -3, 3, -3, 3)
817 mc<-rainbow(ncol(chistabletot))
818 chitable<-chitable[order_chi[,2][1:lim],]
819 cc <- apply(chitable, 1, which.max)
821 #mass<-(rowSums(x)/max(rowSums(x))) * 5
822 maxchi<-norm.vec(maxchi, 0.03, 0.3)
823 rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color= cc,vertex.label.cex = maxchi, vertex.size = 0.1, layout=lo, rescale=FALSE)
824 text3d(lo[,1], lo[,2],lo[,3], rownames(x), cex=maxchi, col=cc)
825 #rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
826 rgl.bg(color = c('white','black'))
827 if (!is.null(movie)) {
829 ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour commencer le film",icon="info",type="ok")
831 movie3d(spin3d(axis=c(0,1,0),rpm=6), movie = 'film_graph', frames = "tmpfilm", duration=10, clean=TRUE, top = TRUE, dir = movie)
832 ReturnVal <- tkmessageBox(title="RGL 3 D",message="Film fini !",icon="info",type="ok")
834 while (rgl.cur() != 0)
840 norm.vec <- function(v, min, max) {
846 fac <- (max-min)/(vr[2]-vr[1])
848 (v-vr[1]) * fac + min
852 vire.nonascii <- function(rnames) {
853 print('vire non ascii')
854 couple <- list(c('é','e'),
876 rnames<-gsub(c[1],c[2], rnames)
884 #layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE)
885 #par(mar=c(1,0,1,0), cex=1)
886 #plot.phylo(tree,label.offset=0.1)
888 #to.plot <- sum.cl[cl.order,1]
889 #d <- barplot(to.plot,horiz=TRUE, names.arg='', axes=FALSE, axisname=FALSE)
890 #text(x=to.plot, y=d[,1], label=round(to.plot,1), adj=1.2)
892 make.afc.attributes <- function(rn, afc.table, contafc, clnb, column = FALSE, x=1, y=2) {
895 afc.res <- afc.table$ligne
896 #tokeep <- which(row.names(afc.res) %in% rn)
897 afc.res <- afc.res[rn,]
899 cor <- afc.res[,debcor:(debcor+nd-1)][,c(x,y)]
901 ctr <- afc.res[,debctr:(debctr+nd-1)][,c(x,y)]
902 massdeb <- (nd*4) + 1
903 mass <- afc.res[,massdeb]
904 chideb <- massdeb + 1
905 chi <- afc.res[,chideb]
906 inertiadeb <- chideb + 1
907 inertia <- afc.res[,inertiadeb]
908 frequence <- rowSums(contafc[rn,])
910 res <- list(frequence=frequence, cor, ctr, mass = mass, chi=chi, inertia=inertia)
915 afctogexf <- function(fileout, toplot, classes, clnb, sizes, nodes.attr=NULL) {
916 toplot <- toplot[,1:3]
918 #toplot <- afc$rowcoord[1:100,1:3]
920 #rownames(toplot)<-afc$rownames[1:100]
921 cc <- rainbow(clnb)[classes]
922 cc <- t(sapply(cc, col2rgb, alpha=TRUE))
923 #sizes <- apply(chistabletot[1:100,], 1, max)
925 nodes <- data.frame(cbind(1:nrow(toplot), rownames(toplot)))
926 colnames(nodes) <- c('id', 'label')
927 nodes[,1] <- as.character(nodes[,1])
928 nodes[,2] <- as.character(nodes[,2])
930 if (! is.null(nodes.attr)) {
931 nodesatt <- as.data.frame(nodes.attr)
933 nodesatt <- data.frame(cbind(toplot[,1],toplot[,2]))
936 edges<-matrix(c(1,1),ncol=2)
937 xmin <- min(toplot[,1])
938 xmax <- max(toplot[,1])
939 ymin <- min(toplot[,2])
940 ymax <- max(toplot[,2])
941 nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
942 nodes<-rbind(nodes, c(nrow(nodes)+1, 'F1'))
943 nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
944 nodes<-rbind(nodes, c(nrow(nodes)+1, 'F2'))
945 nodesatt<-rbind(nodesatt, c(0,0))
946 nodesatt<-rbind(nodesatt, c(0,0))
947 nodesatt<-rbind(nodesatt, c(0,0))
948 nodesatt<-rbind(nodesatt, c(0,0))
949 toplot <- rbind(toplot, c(xmin, 0,0))
950 toplot <- rbind(toplot, c(xmax,0,0))
951 toplot <- rbind(toplot, c(0,ymin,0))
952 toplot <- rbind(toplot, c(0,ymax,0))
953 cc <- rbind(cc, c(255,255,255,1))
954 cc <- rbind(cc, c(255,255,255,1))
955 cc <- rbind(cc, c(255,255,255,1))
956 cc <- rbind(cc, c(255,255,255,1))
957 sizes <- c(sizes, c(0.5, 0.5, 0.5, 0.5))
958 edges <- rbind(edges, c(nrow(nodes)-3, nrow(nodes)-2))
959 edges <- rbind(edges, c(nrow(nodes)-1, nrow(nodes)))
960 write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=cc, position=toplot, size=sizes))
963 simi.to.gexf <- function(fileout, graph.simi, nodes.attr = NULL) {
964 lo <- graph.simi$layout
968 lo <- cbind(lo, rep(0,nrow(lo)))
970 g <- graph.simi$graph
971 nodes <- data.frame(cbind(1:nrow(lo), V(g)$name))
972 colnames(nodes) <- c('id', 'label')
974 if (! is.null(nodes.attr)) {
975 nodesatt <- as.data.frame(nodes.attr)
977 nodesatt <- data.frame(cbind(lo[,1],lo[,2]))
979 edges <- as.data.frame(get.edges(g, c(1:ecount(g))))
980 col <- rep('red', nrow(lo))
981 col <- t(sapply(col, col2rgb, alpha=TRUE))
982 write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))