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$labels <- sprintf('CL %02d',1:clusternb)
26 nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato')
27 jpeg(filename,res=reso)
29 plot(h.chd1, nodePar= nP, edgePar = list(col='gray', lwd=2), horiz=TRUE, center=TRUE, hang= -1)
33 #PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) {
34 # if (Sys.info()["sysname"]=='Darwin') {
36 # height<-height/74.97
37 # quartz(file=filename,type='jpeg',width=width,height=height)
39 # jpeg(filename,width=width,height=height,quality=quality,res=reso)
42 # plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative'))
46 PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL) {
48 if (what == 'coord') {
49 rowcoord <- as.matrix(afc$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$rownames
66 rowcoord <- as.matrix(rowcoord[deb:fin,])
67 chitable<- as.matrix(chisqrtable[deb:fin,])
68 #row_keep <- select_point_nb(chitable,15)
70 if (ncol(rowcoord) == 1) {
71 rowcoord <- t(rowcoord)
73 clnb <- ncol(chisqrtable)
76 classes <- as.matrix(apply(chitable,1,which.max))
77 cex.par <- norm.vec(apply(chitable,1,max), 0.8,3)
78 row.keep <- select.chi.classe(chitable, 60)
79 rowcoord <- rowcoord[row.keep,]
80 classes <- classes[row.keep]
81 cex.par <- cex.par[row.keep]
84 cex.par <- rep(1,clnb)
86 #ntabtot <- cbind(rowcoord, classes)
87 #if (!col) ntabtot <- ntabtot[row_keep,]
88 xlab <- paste('facteur ', x, ' -')
89 ylab <- paste('facteur ', y, ' -')
90 xlab <- paste(xlab,round(afc_table$facteur[x,2],2),sep = ' ')
91 xlab <- paste(xlab,' %%',sep = '')
92 ylab <- paste(ylab,round(afc_table$facteur[y,2],2),sep = ' ')
93 ylab <- paste(ylab,' %%',sep = '')
95 open_file_graph(filename, width = width, height = height)
97 table.in <- rowcoord[order(cex.par, decreasing = TRUE),]
98 classes <- classes[order(cex.par, decreasing = TRUE)]
99 cex.par <- cex.par[order(cex.par, decreasing = TRUE)]
100 table.in <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax))
101 classes <- classes[table.in[,4]]
102 cex.par <- cex.par[table.in[,4]]
103 make_afc_graph(table.in, classes, clnb, xlab, ylab, cex.txt = cex.par, xminmax=c(xmin,xmax), yminmax=c(ymin,ymax))
105 #plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
108 # ntab <- subset(ntabtot,ntabtot[,ncol(ntabtot)] == i)
109 # if (nrow(ntab) != 0)
110 # text(ntab[,x],ntab[,y],rownames(ntab),col=rainbow(clnb)[i])
115 filename.to.svg <- function(filename) {
116 filename <- gsub('.png', '.svg', filename)
120 open_file_graph <- function (filename, width=800, height = 800, quality = 100, svg = FALSE) {
121 if (Sys.info()["sysname"] == 'Darwin') {
123 height <- height/74.97
125 quartz(file = filename, type = 'png', width = width, height = height)
127 svg(filename.to.svg(filename), width=width, height=height)
132 svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
134 png(filename, width=width, height=height)#, quality = quality)
139 #################################################@@
141 overlap <- function(x1, y1, sw1, sh1, boxes) {
142 use.r.layout <- FALSE
144 return(.overlap(x1,y1,sw1,sh1,boxes))
146 if (length(boxes) == 0)
148 for (i in c(last,1:length(boxes))) {
155 overlap <- x1 + sw1 > x2-s
157 overlap <- x2 + sw2 > x1-s
160 overlap <- overlap && (y1 + sh1 > y2-s)
162 overlap <- overlap && (y2 + sh2 > y1-s)
171 .overlap <- function(x11,y11,sw11,sh11,boxes1){
172 .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
174 ########################################################
175 stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {
186 plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim)
189 if (is.null(cex.par)) {
190 size <- rep(0.9, nrow(x))
194 #cols <- rainbow(clnb)
196 for (i in 1:nrow(x)) {
197 rotWord <- runif(1)<rot.per
199 theta <- runif(1,0,2*pi)
202 wid <- strwidth(words[i],cex=size[i])
203 ht <- strheight(words[i],cex=size[i])
206 if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
207 toplot <- rbind(toplot, c(x1, y1, size[i], i))
208 #text(x1,y1,words[i],cex=size[i],offset=0,srt=rotWord*90,
209 # col=cols[classes[i]])
210 boxes[[length(boxes)+1]] <- c(x1-.5*wid,y1-.5*ht,wid,ht)
214 print(paste(words[i], "could not be fit on page. It will not be plotted."))
217 theta <- theta+thetaStep
218 r <- r + rStep*thetaStep/(2*pi)
219 x1 <- x[i,1]+r*cos(theta)
220 y1 <- x[i,2]+r*sin(theta)
224 row.names(toplot) <- words[toplot[,4]]
227 ###############################################################################
229 make_tree_tot <- function (chd) {
233 for (i in 1:length(lf)) {
234 if (!is.null(lf[[i]])) {
235 clus<-gsub(paste('a',i,'a',sep=''),paste('(','a',lf[[i]][1],'a',',','a',lf[[i]][2],'a',')',sep=''),clus)
239 clus <- gsub('a','',clus)
240 tree.cl <- read.tree(text = clus)
241 res<-list(tree.cl = tree.cl, dendro_tuple = dendro_tuple)
245 make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) {
249 for (cl in coordok[,x]) {
251 fcl<-fille(cl,classeuce)
253 dendro <- gsub(paste('a',fi,'a',sep=''),paste('b',i,'b',sep=''),dendro)
256 clnb <- nrow(coordok)
258 for (i in 1:(tcl + 1)) {
259 dendro <- gsub(paste('a',i,'a',sep=''),paste('b',0,'b',sep=''),dendro)
261 dendro <- gsub('b','',dendro)
262 dendro <- gsub('a','',dendro)
263 dendro_tot_cl <- read.tree(text = dendro)
267 dendro <- gsub(paste('\\(',cl,',',cl,'\\)',sep=''),cl,dendro)
271 dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro)
273 dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro)
274 dendro <- gsub(paste('\\(',cl,',',0,'\\)',sep=''),cl,dendro)
278 tree.cl <- read.tree(text = dendro)
279 lab <- tree.cl$tip.label
281 tovire <- which(lab == "0")
282 tree.cl <- drop.tip(tree.cl, tip = tovire)
284 res <- list(tree.cl = tree.cl, dendro_tuple_cut = dendro, dendro_tot_cl = dendro_tot_cl)
288 select_point_nb <- function(tablechi, nb) {
289 chimax<-as.matrix(apply(tablechi,1,max))
290 chimax<-cbind(chimax,1:nrow(tablechi))
291 order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),])
292 row_keep <- order_chi[,2][1:nb]
296 select_point_chi <- function(tablechi, chi_limit) {
297 chimax<-as.matrix(apply(tablechi,1,max))
298 row_keep <- which(chimax >= chi_limit)
302 select.chi.classe <- function(tablechi, nb) {
304 if (nb > nrow(tablechi)) {
307 for (i in 1:ncol(tablechi)) {
308 rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
310 rowkeep <- unique(rowkeep)
315 summary.ca.dm <- function(object, scree = TRUE, ...){
321 if (nd > length(obj$sv)) nd <- length(obj$sv)
323 # principal coordinates:
325 I <- dim(obj$rowcoord)[1] ; J <- dim(obj$colcoord)[1]
326 svF <- matrix(rep(obj$sv[1:K], I), I, K, byrow = TRUE)
327 svG <- matrix(rep(obj$sv[1:K], J), J, K, byrow = TRUE)
328 rpc <- obj$rowcoord[,1:K] * svF
329 cpc <- obj$colcoord[,1:K] * svG
332 r.names <- obj$rownames
334 if (!is.na(sr[1])) r.names[sr] <- paste("(*)", r.names[sr], sep = "")
335 r.mass <- obj$rowmass
336 r.inr <- obj$rowinertia / sum(obj$rowinertia, na.rm = TRUE)
337 r.COR <- matrix(NA, nrow = length(r.names), ncol = nd)
338 colnames(r.COR) <- paste('COR -facteur', 1:nd, sep=' ')
339 r.CTR <- matrix(NA, nrow = length(r.names), ncol = nd)
340 colnames(r.CTR) <- paste('CTR -facteur', 1:nd, sep=' ')
342 r.COR[,i] <- obj$rowmass * rpc[,i]^2 / obj$rowinertia
343 r.CTR[,i] <- obj$rowmass * rpc[,i]^2 / obj$sv[i]^2
345 # cor and quality for supplementary rows
346 if (length(obj$rowsup) > 0){
349 r.COR[i0,i] <- obj$rowmass[i0] * rpc[i0,i]^2
355 c.names <- obj$colnames
357 if (!is.na(sc[1])) c.names[sc] <- paste("(*)", c.names[sc], sep = "")
358 c.mass <- obj$colmass
359 c.inr <- obj$colinertia / sum(obj$colinertia, na.rm = TRUE)
360 c.COR <- matrix(NA, nrow = length(c.names), ncol = nd)
361 colnames(c.COR) <- paste('COR -facteur', 1:nd, sep=' ')
362 c.CTR <- matrix(NA, nrow = length(c.names), ncol = nd)
363 colnames(c.CTR) <- paste('CTR -facteur', 1:nd, sep=' ')
366 c.COR[,i] <- obj$colmass * cpc[,i]^2 / obj$colinertia
367 c.CTR[,i] <- obj$colmass * cpc[,i]^2 / obj$sv[i]^2
369 if (length(obj$colsup) > 0){
372 c.COR[i0,i] <- obj$colmass[i0] * cpc[i0,i]^2
380 values2 <- 100*(obj$sv^2)/sum(obj$sv^2)
381 values3 <- cumsum(100*(obj$sv^2)/sum(obj$sv^2))
382 scree.out <- cbind(values, values2, values3)
391 obj$facteur <- scree.out
395 create_afc_table <- function(x) {
397 facteur.table <- as.matrix(x$facteur)
398 nd <- ncol(x$colcoord)
399 rownames(facteur.table) <- paste('facteur',1:nrow(facteur.table),sep = ' ')
400 colnames(facteur.table) <- c('Valeurs propres', 'Pourcentages', 'Pourcentage cumules')
401 ligne.table <- as.matrix(x$rowcoord)
402 rownames(ligne.table) <- x$rownames
403 colnames(ligne.table) <- paste('Coord. facteur', 1:nd, sep=' ')
404 tmp <- as.matrix(x$rowcrl)
405 colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ')
406 ligne.table <- cbind(ligne.table,tmp)
407 ligne.table <- cbind(ligne.table, x$r.COR)
408 ligne.table <- cbind(ligne.table, x$r.CTR)
409 ligne.table <- cbind(ligne.table, mass = x$rowmass)
410 ligne.table <- cbind(ligne.table, chi.distance = x$rowdist)
411 ligne.table <- cbind(ligne.table, inertie = x$rowinertia)
412 colonne.table <- x$colcoord
413 rownames(colonne.table) <- paste('classe', 1:(nrow(colonne.table)),sep=' ')
414 colnames(colonne.table) <- paste('Coord. facteur', 1:nd, sep=' ')
415 tmp <- as.matrix(x$colcrl)
416 colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ')
417 colonne.table <- cbind(colonne.table, tmp)
418 colonne.table <- cbind(colonne.table, x$c.COR)
419 colonne.table <- cbind(colonne.table, x$c.CTR)
420 colonne.table <- cbind(colonne.table, mass = x$colmass)
421 colonne.table <- cbind(colonne.table, chi.distance = x$coldist)
422 colonne.table <- cbind(colonne.table, inertie = x$colinertia)
423 res <- list(facteur = facteur.table, ligne = ligne.table, colonne = colonne.table)
427 make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
429 rain <- rainbow(clnb)
432 for (my.color in rain) {
433 my.color <- col2rgb(my.color)
434 if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
435 tochange <- append(tochange, compt)
439 if (!is.null(tochange)) {
440 gr.col <- grey.colors(length(tochange))
442 for (val in tochange) {
443 rain[val] <- gr.col[compt]
447 cl.color <- rain[classes]
451 plot(toplot[,1],toplot[,2], pch='', xlab = xlab, ylab = ylab, xlim=xminmax, ylim = yminmax)
452 abline(h=0, v=0, lty = 'dashed')
453 if (is.null(cex.txt))
454 text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, offset=0)
456 text(toplot[,1],toplot[,2],rownames(toplot),col=cl.color, cex = cex.txt, offset=0)
463 plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) {
464 classes<-classes[classes!=0]
465 classes<-as.factor(classes)
466 sum.cl<-as.matrix(summary(classes))
467 sum.cl<-(sum.cl/colSums(sum.cl)*100)
468 sum.cl<-round(sum.cl,2)
469 sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
470 tree.order<- as.numeric(tree$tip.label)
472 col = rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)]
474 col.pie <- rainbow(nrow(sum.cl))
475 #col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
479 col.pie <- rep('grey',nrow(sum.cl))
482 for (i in 1:nrow(sum.cl)) vec.mat<-append(vec.mat,1)
484 for (i in 1:nrow(sum.cl)) {
485 vec.mat<-append(vec.mat,v)
491 layout(matrix(vec.mat,nrow(sum.cl),2),widths=c(3,1))
493 layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE)
496 par(mar=c(0,0,0,0),cex=1)
499 tree$tip.label <- lab
501 tree[[2]]<-paste('classe ',tree[[2]])
503 plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
504 #cl.order <- as.numeric(label.ori)
506 #for (i in 1:nrow(sum.cl)) {
509 for (i in rev(tree.order)) {
510 par(mar=c(0,0,1,0),cex=0.7)
511 pie(sum.cl[i,],col=c(col.pie[i],'white'),radius = 1, labels='', clockwise=TRUE, main = paste('classe ',i,' - ',sum.cl[i,1],'%' ))
516 to.plot <- sum.cl[tree.order,1]
517 d <- barplot(to.plot,horiz=TRUE, col=col.bars, names.arg='', axes=FALSE, axisname=FALSE)
518 text(x=to.plot, y=d[,1], label=paste(round(to.plot,1),'%'), adj=1.2)
521 if (!from.cmd) dev.off()
524 #tree <- tree.cut1$tree.cl
526 plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), cmd=FALSE) {
527 tree.order<- as.numeric(tree$tip.label)
529 layout(matrix(c(1,2,3),1,byrow=TRUE), widths=lay.width,TRUE)
530 par(mar=c(3,0,2,0),cex=1)
533 tree$tip.label <- lab
535 tree[[2]]<-paste('classe ',tree[[2]])
537 to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
539 col <- rainbow(ncol(to.plot))
540 col.bars <- rainbow(nrow(to.plot))
543 col.bars <- grey.colors(nrow(to.plot),0,0.8)
545 col <- col[tree.order]
546 plot.phylo(tree,label.offset=0.1,tip.col=col)
549 d <- barplot(to.plot,horiz=TRUE, col=col.bars, beside=TRUE, names.arg='', space = c(0.1,0.6), axisname=FALSE)
554 lcoord <- apply(cc, 1, mean)
556 if (min(to.plot) < 0) {
557 amp <- abs(max(to.plot) - min(to.plot))
564 d <- signif(amp%/%10,1)
566 mn <- round(min(to.plot))
567 mx <- round(max(to.plot))
569 if ((i/d) == (i%/%d)) {
574 plot(0, axes = FALSE, pch = '')
575 legend(x = 'center' , rownames(to.plot), fill = col.bars)
582 plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) {
584 if (is.null(debsup)) {
585 tab.toplot<-afctable[1:(debet+1),]
586 chitab<-chistabletot[1:(debet+1),]
588 tab.toplot<-afctable[1:(debsup+1),]
589 chitab<-chistabletot[1:(debsup+1),]
591 rkeep<-select_point_chi(chitab,chilim)
592 tab.toplot<-tab.toplot[rkeep,]
593 chitab<-chitab[rkeep,]
594 dm<-dist(tab.toplot,diag=TRUE,upper=TRUE)
595 cn<-rownames(tab.toplot)
596 cl.toplot<-apply(chitab,1,which.max)
597 col<-rainbow(ncol(tab.toplot))[cl.toplot]
599 g1 <- graph.adjacency(as.matrix(dm), mode = 'lower', weighted = TRUE)
600 g.max<-minimum.spanning.tree(g1)
601 we<-(rowSums(tab.toplot)/max(rowSums(tab.toplot)))*2
602 #lo <- layout.fruchterman.reingold(g.max,dim=nd)
603 lo<- layout.kamada.kawai(g.max,dim=nd)
604 print(nrow(tab.toplot))
610 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)
611 } else if (nd == 2) {
612 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)
617 make.simi.afc <- function(x,chitable,lim=0, alpha = 0.1, movie = NULL) {
619 chimax<-as.matrix(apply(chitable,1,max))
620 chimax<-as.matrix(chimax[,1][1:nrow(x)])
621 chimax<-cbind(chimax,1:nrow(x))
622 order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),])
623 if ((lim == 0) || (lim>nrow(x))) lim <- nrow(x)
624 x<-x[order_chi[,2][1:lim],]
625 maxchi <- chimax[order_chi[,2][1:lim],1]
626 #-------------------------------------------------------
628 distm<-dist(x,diag=TRUE)
629 distm<-as.matrix(distm)
630 g1<-graph.adjacency(distm,mode='lower',weighted=TRUE)
631 g1<-minimum.spanning.tree(g1)
632 lo<-layout.kamada.kawai(g1,dim=3)
633 lo <- layout.norm(lo, -3, 3, -3, 3, -3, 3)
634 mc<-rainbow(ncol(chistabletot))
635 chitable<-chitable[order_chi[,2][1:lim],]
636 cc <- apply(chitable, 1, which.max)
638 #mass<-(rowSums(x)/max(rowSums(x))) * 5
639 maxchi<-norm.vec(maxchi, 0.03, 0.3)
640 rglplot(g1,vertex.label = vire.nonascii(rownames(x)),vertex.label.color= cc,vertex.label.cex = maxchi, vertex.size = 0.1, layout=lo, rescale=FALSE)
641 text3d(lo[,1], lo[,2],lo[,3], rownames(x), cex=maxchi, col=cc)
642 #rgl.spheres(lo, col = cc, radius = maxchi, alpha = alpha)
643 rgl.bg(color = c('white','black'))
644 if (!is.null(movie)) {
646 ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour commencer le film",icon="info",type="ok")
648 movie3d(spin3d(axis=c(0,1,0),rpm=6), movie = 'film_graph', frames = "tmpfilm", duration=10, clean=TRUE, top = TRUE, dir = movie)
649 ReturnVal <- tkmessageBox(title="RGL 3 D",message="Film fini !",icon="info",type="ok")
651 while (rgl.cur() != 0)
657 norm.vec <- function(v, min, max) {
663 fac <- (max-min)/(vr[2]-vr[1])
665 (v-vr[1]) * fac + min
669 vire.nonascii <- function(rnames) {
670 print('vire non ascii')
671 couple <- list(c('é','e'),
693 rnames<-gsub(c[1],c[2], rnames)
701 #layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE)
702 #par(mar=c(1,0,1,0), cex=1)
703 #plot.phylo(tree,label.offset=0.1)
705 #to.plot <- sum.cl[cl.order,1]
706 #d <- barplot(to.plot,horiz=TRUE, names.arg='', axes=FALSE, axisname=FALSE)
707 #text(x=to.plot, y=d[,1], label=round(to.plot,1), adj=1.2)