############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() #} PlotDendroCut <- function(chd,filename,reso,clusternb) { h.chd <- as.hclust(chd) memb <- cutree(h.chd, k = clusternb) cent <- NULL for(k in 1:clusternb){ cent <- rbind(cent, k) } h.chd1 <- hclust(dist(cent)^2, method = 'cen', members = table(memb)) h.chd1$labels <- sprintf('CL %02d',1:clusternb) nP <- list(col=3:2, cex=c(2.0, 0.75), pch= 21:22, bg= c('light blue', 'pink'),lab.cex = 0.75, lab.col = 'tomato') jpeg(filename,res=reso) par(cex=PARCEX) plot(h.chd1, nodePar= nP, edgePar = list(col='gray', lwd=2), horiz=TRUE, center=TRUE, hang= -1) dev.off() } #PlotAfc<- function(afc, filename, width=800, height=800, quality=100, reso=200, toplot=c('all','all'), PARCEX=PARCEX) { # if (Sys.info()["sysname"]=='Darwin') { # width<-width/74.97 # height<-height/74.97 # quartz(file=filename,type='jpeg',width=width,height=height) # } else { # jpeg(filename,width=width,height=height,quality=quality,res=reso) # } # par(cex=PARCEX) # plot(afc,what=toplot,labels=c(1,1),contrib=c('absolute','relative')) # dev.off() #} PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axetoplot=c(1,2), deb=0,fin=0, width=900, height=900, quality=100, reso=200, parcex=PARCEX, xlab = NULL, ylab = NULL, xmin=NULL, xmax=NULL, ymin=NULL, ymax=NULL, active = TRUE) { if (col) { if (what == 'coord') { rowcoord <- as.matrix(afc$colcoord) } else { rowcoord <- as.matrix(afc$colcrl) } } else { if (what == 'coord') { rowcoord <- as.matrix(afc$rowcoord) } else { rowcoord <- as.matrix(afc$rowcrl) } } x <- axetoplot[1] y <- axetoplot[2] if (col) rownames(rowcoord) <- afc$colnames if (!col){ rownames(rowcoord) <- afc$rownames rowcoord <- as.matrix(rowcoord[deb:fin,]) chitable<- as.matrix(chisqrtable[deb:fin,]) #row_keep <- select_point_nb(chitable,15) } if (ncol(rowcoord) == 1) { rowcoord <- t(rowcoord) } clnb <- ncol(chisqrtable) if (!col) { classes <- as.matrix(apply(chitable,1,which.max)) cex.par <- norm.vec(apply(chitable,1,max), 0.8,3) row.keep <- select.chi.classe(chitable, 80, active=active) rowcoord <- rowcoord[row.keep,] classes <- classes[row.keep] cex.par <- cex.par[row.keep] } else { classes <- 1:clnb cex.par <- rep(1,clnb) } if (is.null(xmin)) { table.in <- rowcoord xminmax <- c(min(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,1], na.rm = TRUE)), max(table.in[,1], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,1], na.rm = TRUE))) xmin <- xminmax[1] xmax <- xminmax[2] yminmax <- c(min(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * min(table.in[,2], na.rm = TRUE)), max(table.in[,2], na.rm = TRUE) + ((max(cex.par)/10) * max(table.in[,2], na.rm = TRUE))) ymin <- yminmax[1] ymax <- yminmax[2] } #ntabtot <- cbind(rowcoord, classes) #if (!col) ntabtot <- ntabtot[row_keep,] xlab <- paste('facteur ', x, ' -') ylab <- paste('facteur ', y, ' -') xlab <- paste(xlab,round(afc_table$facteur[x,2],2),sep = ' ') xlab <- paste(xlab,' %%',sep = '') ylab <- paste(ylab,round(afc_table$facteur[y,2],2),sep = ' ') ylab <- paste(ylab,' %%',sep = '') open_file_graph(filename, width = width, height = height) par(cex=PARCEX) table.in <- rowcoord[order(cex.par, decreasing = TRUE),] classes <- classes[order(cex.par, decreasing = TRUE)] cex.par <- cex.par[order(cex.par, decreasing = TRUE)] table.out <- stopoverlap(table.in, cex.par=cex.par, xlim = c(xmin,xmax), ylim = c(ymin,ymax)) table.in <- table.out$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) { filename <- gsub('.png', '.svg', filename) return(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 if (!svg) { quartz(file = filename, type = 'png', width = width, height = height) } else { svg(filename.to.svg(filename), width=width, height=height) } } else { if (svg) { svg(filename.to.svg(filename), width=width/74.97, height=height/74.97) } else { png(filename, width=width, height=height)#, quality = quality) } } } #################################################@@ #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){ if (as.character(packageVersion('wordcloud')) >= '2.6') { .Call("_wordcloud_is_overlap", x11,y11,sw11,sh11,boxes1) } else { .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)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)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$list_fille clus<-'a1a;' for (i in 1:length(lf)) { if (!is.null(lf[[i]])) { clus<-gsub(paste('a',i,'a',sep=''),paste('(','a',lf[[i]][1],'a',',','a',lf[[i]][2],'a',')',sep=''),clus) } } dendro_tuple <- clus clus <- gsub('a','',clus) tree.cl <- read.tree(text = clus) res<-list(tree.cl = tree.cl, dendro_tuple = dendro_tuple) res } make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) { library(ape) dendro<-dendro_in i <- 0 for (cl in coordok[,x]) { i <- i + 1 fcl<-fille(cl,classeuce) for (fi in fcl) { dendro <- gsub(paste('a',fi,'a',sep=''),paste('b',i,'b',sep=''),dendro) } } clnb <- nrow(coordok) tcl=((nbt+1) *2) - 2 for (i in 1:(tcl + 1)) { dendro <- gsub(paste('a',i,'a',sep=''),paste('b',0,'b',sep=''),dendro) } dendro <- gsub('b','',dendro) dendro <- gsub('a','',dendro) dendro_tot_cl <- read.tree(text = dendro) #FIXME for (i in 1:100) { for (cl in 1:clnb) { dendro <- gsub(paste('\\(',cl,',',cl,'\\)',sep=''),cl,dendro) } } for (i in 1:100) { dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro) for (cl in 1:clnb) { dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro) dendro <- gsub(paste('\\(',cl,',',0,'\\)',sep=''),cl,dendro) } } print(dendro) tree.cl <- read.tree(text = dendro) lab <- tree.cl$tip.label if ("0" %in% lab) { tovire <- which(lab == "0") tree.cl <- drop.tip(tree.cl, tip = tovire) } res <- list(tree.cl = tree.cl, dendro_tuple_cut = dendro, dendro_tot_cl = dendro_tot_cl) res } select_point_nb <- function(tablechi, nb) { chimax<-as.matrix(apply(tablechi,1,max)) chimax<-cbind(chimax,1:nrow(tablechi)) order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),]) row_keep <- order_chi[,2][1:nb] row_keep } select_point_chi <- function(tablechi, chi_limit) { chimax<-as.matrix(apply(tablechi,1,max)) row_keep <- which(chimax >= chi_limit) 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 nd <- obj$nd if (is.na(nd)){ nd <- 2 } else { if (nd > length(obj$sv)) nd <- length(obj$sv) } # principal coordinates: K <- nd I <- dim(obj$rowcoord)[1] ; J <- dim(obj$colcoord)[1] svF <- matrix(rep(obj$sv[1:K], I), I, K, byrow = TRUE) svG <- matrix(rep(obj$sv[1:K], J), J, K, byrow = TRUE) rpc <- obj$rowcoord[,1:K] * svF cpc <- obj$colcoord[,1:K] * svG # rows: r.names <- obj$rownames sr <- obj$rowsup if (!is.na(sr[1])) r.names[sr] <- paste("(*)", r.names[sr], sep = "") r.mass <- obj$rowmass r.inr <- obj$rowinertia / sum(obj$rowinertia, na.rm = TRUE) r.COR <- matrix(NA, nrow = length(r.names), ncol = nd) colnames(r.COR) <- paste('COR -facteur', 1:nd, sep=' ') r.CTR <- matrix(NA, nrow = length(r.names), ncol = nd) colnames(r.CTR) <- paste('CTR -facteur', 1:nd, sep=' ') for (i in 1:nd){ r.COR[,i] <- obj$rowmass * rpc[,i]^2 / obj$rowinertia r.CTR[,i] <- obj$rowmass * rpc[,i]^2 / obj$sv[i]^2 } # cor and quality for supplementary rows if (length(obj$rowsup) > 0){ i0 <- obj$rowsup for (i in 1:nd){ r.COR[i0,i] <- obj$rowmass[i0] * rpc[i0,i]^2 r.CTR[i0,i] <- NA } } # columns: c.names <- obj$colnames sc <- obj$colsup if (!is.na(sc[1])) c.names[sc] <- paste("(*)", c.names[sc], sep = "") c.mass <- obj$colmass c.inr <- obj$colinertia / sum(obj$colinertia, na.rm = TRUE) c.COR <- matrix(NA, nrow = length(c.names), ncol = nd) colnames(c.COR) <- paste('COR -facteur', 1:nd, sep=' ') c.CTR <- matrix(NA, nrow = length(c.names), ncol = nd) colnames(c.CTR) <- paste('CTR -facteur', 1:nd, sep=' ') for (i in 1:nd) { c.COR[,i] <- obj$colmass * cpc[,i]^2 / obj$colinertia c.CTR[,i] <- obj$colmass * cpc[,i]^2 / obj$sv[i]^2 } if (length(obj$colsup) > 0){ i0 <- obj$colsup for (i in 1:nd){ c.COR[i0,i] <- obj$colmass[i0] * cpc[i0,i]^2 c.CTR[i0,i] <- NA } } # scree plot: if (scree) { values <- obj$sv^2 values2 <- 100*(obj$sv^2)/sum(obj$sv^2) values3 <- cumsum(100*(obj$sv^2)/sum(obj$sv^2)) scree.out <- cbind(values, values2, values3) } else { scree.out <- NA } obj$r.COR <- r.COR obj$r.CTR <- r.CTR obj$c.COR <- c.COR obj$c.CTR <- c.CTR obj$facteur <- scree.out return(obj) } create_afc_table <- function(x) { #x = afc facteur.table <- as.matrix(x$facteur) nd <- ncol(x$colcoord) rownames(facteur.table) <- paste('facteur',1:nrow(facteur.table),sep = ' ') colnames(facteur.table) <- c('Valeurs propres', 'Pourcentages', 'Pourcentage cumules') ligne.table <- as.matrix(x$rowcoord) rownames(ligne.table) <- x$rownames colnames(ligne.table) <- paste('Coord. facteur', 1:nd, sep=' ') tmp <- as.matrix(x$rowcrl) colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ') ligne.table <- cbind(ligne.table,tmp) ligne.table <- cbind(ligne.table, x$r.COR) ligne.table <- cbind(ligne.table, x$r.CTR) ligne.table <- cbind(ligne.table, mass = x$rowmass) ligne.table <- cbind(ligne.table, chi.distance = x$rowdist) ligne.table <- cbind(ligne.table, inertie = x$rowinertia) colonne.table <- x$colcoord rownames(colonne.table) <- paste('classe', 1:(nrow(colonne.table)),sep=' ') colnames(colonne.table) <- paste('Coord. facteur', 1:nd, sep=' ') tmp <- as.matrix(x$colcrl) colnames(tmp) <- paste('Corr. facteur', 1:nd, sep=' ') colonne.table <- cbind(colonne.table, tmp) colonne.table <- cbind(colonne.table, x$c.COR) colonne.table <- cbind(colonne.table, x$c.CTR) colonne.table <- cbind(colonne.table, mass = x$colmass) colonne.table <- cbind(colonne.table, chi.distance = x$coldist) colonne.table <- cbind(colonne.table, inertie = x$colinertia) res <- list(facteur = facteur.table, ligne = ligne.table, colonne = colonne.table) res } 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 for (val in tochange) { colors[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 } 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, offset=0) else #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$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { tree$tip.label<-paste('classe ',tree$tip.label) } 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$tip.label)] colcloud <- rainbow(length(sum.cl)) } par(mar=c(0,0,0,0)) label.ori<-tree$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { tree$tip.label<-paste('classe ',tree$tip.label) } plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro) for (i in rev(tree.order)) { par(mar=c(0,0,1,0),cex=0.9) wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(2.5, 0.5), random.order=FALSE, colors = colcloud[i]) } } plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) { classes<-classes[classes!=0] classes<-as.factor(classes) sum.cl<-as.matrix(summary(classes, maxsum=1000000)) sum.cl<-(sum.cl/colSums(sum.cl)*100) sum.cl<-round(sum.cl,2) sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1])) tree.order<- as.numeric(tree$tip.label) if (! bw) { col <- rainbow(nrow(sum.cl))[as.numeric(tree$tip.label)] col <- del.yellow(col) col.bars <- col col.pie <- rainbow(nrow(sum.cl)) col.pie <- del.yellow(col.pie) #col.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])] } else { col = 'black' col.bars = 'grey' col.pie <- rep('grey',nrow(sum.cl)) } vec.mat<-NULL for (i in 1:nrow(sum.cl)) vec.mat<-append(vec.mat,1) v<-2 for (i in 1:nrow(sum.cl)) { vec.mat<-append(vec.mat,v) v<-v+1 } par(mar=c(0,0,0,0)) if (tclasse) { if (! histo) { layout(matrix(vec.mat,nrow(sum.cl),2),widths=c(3,1)) } else { layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE) } } par(mar=c(0,0,0,0),cex=1) label.ori<-tree$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { tree$tip.label<-paste('classe ',tree$tip.label) } plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro) #cl.order <- as.numeric(label.ori) #sum.cl[cl.order,1] #for (i in 1:nrow(sum.cl)) { if (tclasse) { if (! histo) { for (i in rev(tree.order)) { par(mar=c(0,0,1,0),cex=0.7) pie(sum.cl[i,],col=c(col.pie[i],'white'),radius = 1, labels='', clockwise=TRUE, main = paste('classe ',i,' - ',sum.cl[i,1],'%' )) } } else { par(cex=0.7) par(mar=c(0,0,0,1)) to.plot <- sum.cl[tree.order,1] d <- barplot(to.plot,horiz=TRUE, col=col.bars, names.arg='', axes=FALSE, axisname=FALSE) text(x=to.plot, y=d[,1], label=paste(round(to.plot,1),'%'), adj=1.2) } } if (!from.cmd) dev.off() tree[[2]]<-label.ori } #tree <- tree.cut1$tree.cl #to.plot <- di plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, direction = 'rightwards', cmd=FALSE) { tree.order<- as.numeric(tree$tip.label) if (!is.null(classes)) { classes<-classes[classes!=0] classes<-as.factor(classes) sum.cl<-as.matrix(summary(classes, maxsum=1000000)) sum.cl<-(sum.cl/colSums(sum.cl)*100) sum.cl<-round(sum.cl,2) sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1])) } par(mar=c(0,0,0,0)) if (direction == 'rightwards') { srt <- 0 adj <- NULL horiz <- TRUE if (!is.null(classes)) { matlay <- matrix(c(1,2,3,4),1,byrow=TRUE) lay.width <- c(3,2,3,2) } else { matlay <- matrix(c(1,2,3),1,byrow=TRUE) } } else { srt <- 90 adj <- 0.5 horiz <- FALSE if (!is.null(classes)) { matlay <- matrix(c(1,2,3,4,4,4),3) } else { matlay <- matrix(c(1,2,3,3),2) } lay.width <- c(5,2) } layout(matlay, widths=lay.width,TRUE) par(mar=c(3,0,2,4),cex=1) label.ori<-tree$tip.label if (!is.null(lab)) { tree$tip.label <- lab } else { tree$tip.label<-paste('classe ',tree$tip.label) } 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 <- 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=0.2,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=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)] cc <- cbind(c1,c2) lcoord <- apply(cc, 1, mean) abline(h=lcoord) if (min(to.plot) < 0) { amp <- abs(max(to.plot) - min(to.plot)) } else { amp <- max(to.plot) } if (amp < 10) { d <- 2 } else { d <- signif(amp%/%10,1) } mn <- round(min(to.plot)) mx <- round(max(to.plot)) for (i in mn:mx) { if ((i/d) == (i%/%d)) { abline(v=i,lty=3) } } par(mar=c(0,0,0,0)) plot(0, axes = FALSE, pch = '') legend(x = 'center' , rev(rownames(to.plot)), fill = rev(col.bars)) if (!cmd) { dev.off() } tree[[2]]<-label.ori } plot.spec <- function(spec, nb.word = 20) { word.to.plot <- NULL word.size <- NULL rno <- rownames(spec) cn <- colnames(spec) if (nb.word > length(rno)) {nb.word <- length(rno)} for (val in 1:ncol(spec)) { rn <- rno[order(spec[,val], decreasing=T)][1:nb.word] score <- spec[order(spec[,val], decreasing=T),val][1:nb.word] word.to.plot <- cbind(word.to.plot, rn) word.size <- cbind(word.size, score) } mat.lay <- matrix(1:ncol(spec),nrow=1,ncol=ncol(spec)) layout(mat.lay) for (i in 1:ncol(spec)) { col <- ifelse((i %% 2) == 0, 'red', 'blue') par(mar=c(0,0,1,0),cex=0.7) yval <- 1.1 plot(0,0,pch='', axes = FALSE) vcex <- norm.vec(word.size[,i], 2, 3) text(-0.9, -0.5, cn[i], cex = 1, adj=0, srt=90, col='black') for (j in 1:length(word.size[,i])) { yval <- yval-(strheight(word.to.plot[j,i],cex=vcex[j])+0.01) text(-0.9, yval, word.to.plot[j,i], cex = vcex[j], col = col, adj=0) } } } plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) { load(rdata) if (is.null(debsup)) { tab.toplot<-afctable[1:(debet+1),] chitab<-chistabletot[1:(debet+1),] } else { tab.toplot<-afctable[1:(debsup+1),] chitab<-chistabletot[1:(debsup+1),] } rkeep<-select_point_chi(chitab,chilim) tab.toplot<-tab.toplot[rkeep,] chitab<-chitab[rkeep,] dm<-dist(tab.toplot,diag=TRUE,upper=TRUE) cn<-rownames(tab.toplot) cl.toplot<-apply(chitab,1,which.max) col<-rainbow(ncol(tab.toplot))[cl.toplot] library(igraph) g1 <- graph.adjacency(as.matrix(dm), mode = 'lower', weighted = TRUE) g.max<-minimum.spanning.tree(g1) we<-(rowSums(tab.toplot)/max(rowSums(tab.toplot)))*2 #lo <- layout.fruchterman.reingold(g.max,dim=nd) lo<- layout.kamada.kawai(g.max,dim=nd) print(nrow(tab.toplot)) print(nrow(chitab)) print(length(we)) print(length(col)) print(length(cn)) if (nd == 3) { 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) } else if (nd == 2) { 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) } } make.simi.afc <- function(x,chitable,lim=0, alpha = 0.1, movie = NULL) { library(igraph) library(rgl) chimax<-as.matrix(apply(chitable,1,max)) chimax<-as.matrix(chimax[,1][1:nrow(x)]) chimax<-cbind(chimax,1:nrow(x)) order_chi<-as.matrix(chimax[order(chimax[,1],decreasing = TRUE),]) if ((lim == 0) || (lim>nrow(x))) lim <- nrow(x) x<-x[order_chi[,2][1:lim],] maxchi <- chimax[order_chi[,2][1:lim],1] #------------------------------------------------------- limit<-nrow(x) distm<-dist(x,diag=TRUE) distm<-as.matrix(distm) g1<-graph.adjacency(distm,mode='lower',weighted=TRUE) g1<-minimum.spanning.tree(g1) lo<-layout.kamada.kawai(g1,dim=3) lo <- layout.norm(lo, -3, 3, -3, 3, -3, 3) mc<-rainbow(ncol(chistabletot)) chitable<-chitable[order_chi[,2][1:lim],] cc <- apply(chitable, 1, which.max) 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= 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) ReturnVal <- tkmessageBox(title="RGL 3 D",message="Cliquez pour commencer le film",icon="info",type="ok") movie3d(spin3d(axis=c(0,1,0),rpm=6), movie = 'film_graph', frames = "tmpfilm", duration=10, clean=TRUE, top = TRUE, dir = movie) ReturnVal <- tkmessageBox(title="RGL 3 D",message="Film fini !",icon="info",type="ok") } while (rgl.cur() != 0) Sys.sleep(1) } # from igraph norm.vec <- function(v, min, max) { vr <- range(v) if (vr[1]==vr[2]) { fac <- 1 } else { fac <- (max-min)/(vr[2]-vr[1]) } (v-vr[1]) * fac + min } vire.nonascii <- function(rnames) { print('vire non ascii') couple <- list(c('é','e'), c('è','e'), c('ê','e'), c('ë','e'), c('î','i'), c('ï','i'), c('ì','i'), c('à','a'), c('â','a'), c('ä','a'), c('á','a'), c('ù','u'), c('û','u'), c('ü','u'), c('ç','c'), c('ò','o'), c('ô','o'), c('ö','o'), c('ñ','n') ) for (c in couple) { rnames<-gsub(c[1],c[2], rnames) } rnames } #par(mar=c(0,0,0,0)) #layout(matrix(c(1,2),1,byrow=TRUE), widths=c(3,2),TRUE) #par(mar=c(1,0,1,0), cex=1) #plot.phylo(tree,label.offset=0.1) #par(mar=c(0,0,0,1)) #to.plot <- sum.cl[cl.order,1] #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$layout,-10,10,-10,10,-10,10) #print(layout) V(g)$x <- layout[,1] V(g)$y <- layout[,2] if (ncol(layout) == 3) { V(g)$z <- layout[,3] } E(g)$weight <- graph.simi$we.width 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$edges, edgesfile, sep='\t', row.names=FALSE) } if (is.null(edgesfile) & is.null(nodesfile)) { df } } graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) { require(igraph) g <- graph layout <- layout.norm(layout,-5,5,-5,5,-5,5) V(g)$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 } }