X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=Rscripts%2FRgraph.R;h=8407e319d5bd046c1a3f6a73f6c02d7a3f947b16;hp=4759448ed18c2a8277abd37158b3985e1f77a416;hb=097e7017a8f1c597573e7baf9d23553b274eabd1;hpb=22cd27b2bbe9ab1ffa7ef06fa764b5147ae17dad diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R index 4759448..8407e31 100644 --- a/Rscripts/Rgraph.R +++ b/Rscripts/Rgraph.R @@ -1,20 +1,20 @@ ############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) { +PlotDendroCut <- function(chd,filename,reso,clusternb) { h.chd <- as.hclust(chd) memb <- cutree(h.chd, k = clusternb) cent <- NULL @@ -30,20 +30,20 @@ PlotDendroCut <- function(chd,filename,reso,clusternb) { 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$colcoord) @@ -59,7 +59,6 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto } x <- axetoplot[1] y <- axetoplot[2] - if (col) rownames(rowcoord) <- afc$colnames if (!col){ @@ -73,20 +72,59 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto } 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) { @@ -96,12 +134,14 @@ 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 { @@ -110,6 +150,218 @@ open_file_graph <- function (filename, width=800, height = 800, quality = 100, s } } +#################################################@@ +#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 @@ -146,12 +398,12 @@ make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) { 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) @@ -183,6 +435,36 @@ select_point_chi <- function(tablechi, 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 @@ -296,50 +578,209 @@ create_afc_table <- function(x) { 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$tip.label + if (!is.null(lab)) { + tree$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$tip.label) + } + plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro) + for (i in rev(tree.order)) { + par(mar=c(0,0,1,0),cex=0.9) + wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(2.5, 0.5), random.order=FALSE, colors = colcloud[i]) + } +} + plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, from.cmd=FALSE, bw=FALSE, lab = NULL, tclasse=TRUE) { classes<-classes[classes!=0] classes<-as.factor(classes) - sum.cl<-as.matrix(summary(classes)) + sum.cl<-as.matrix(summary(classes, maxsum=1000000)) sum.cl<-(sum.cl/colSums(sum.cl)*100) sum.cl<-round(sum.cl,2) sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1])) tree.order<- as.numeric(tree$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' @@ -362,11 +803,11 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f } } 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) @@ -391,30 +832,71 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f } #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) - label.ori<-tree[[2]] + 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[[2]]<-paste('classe ',tree[[2]]) + 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.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)] @@ -440,13 +922,43 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2 } 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() } 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)) { @@ -484,6 +996,7 @@ plot.alceste.graph <- function(rdata,nd=3,layout='fruke', chilim = 2) { 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)) @@ -505,8 +1018,9 @@ make.simi.afc <- function(x,chitable,lim=0, alpha = 0.1, movie = NULL) { 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) @@ -573,3 +1087,189 @@ vire.nonascii <- function(rnames) { #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 + } +} +