--- /dev/null
+
+
+load('mariagepourtousnov-jui_corpus_corpus_1/mariagepourtousnov-jui_corpus_alceste_2/RData.RData')
+load('mariagegaynov-jui_corpus_corpus_1/mariagegaynov-jui_corpus_alceste_3/RData.RData')
+load('mariagehomonov-jui_corpus_corpus_1/mariagehomonov-jui_corpus_alceste_2/RData.RData')
+
+dpt <- chistabletot[tc,]
+#dpt <- chistabletot[debet:nrow(chistabletot),]
+dd <-rownames(dpt)
+dd <- strptime(dd, "*date_%Y-%m-%d")
+dd <- strptime(dd, "%Y-%m-%d")
+dd <- cbind(as.character(dd), dpt)
+dd <- dd[order(dd[,1]),]
+dd <- add.missing.date(dd,c.dates = 1, datedeb=c(07,11,2012), datefin=c(31,07,2013))
+
+#tot <- afctable[debet:nrow(afctable),]
+tot <- afctable[tc,]
+tt <- rownames(tot)
+tt <- strptime(tt, "*date_%Y-%m-%d")
+tt <- strptime(tt, "%Y-%m-%d")
+tt <- cbind(as.character(tt), tot)
+tt <- tt[order(tt[,1]),]
+tt <- add.missing.date(tt, c.dates = 1, datedeb=c(07,11,2012), datefin=c(31,07,2013))
+
+rn <- tt[,1]
+tt <- tt[,-1]
+tt <- apply(tt, 2, as.numeric)
+rownames(tt) <- rn
+tcp <- rowSums(tt)
+ptc <- tcp/sum(tcp)
+
+ptt <- prop.table(as.matrix(tt), 1)
+
+tcl <- table(classes)
+z <- which(names(tcl)=="0")
+if (length(z) != 0) {tcl <- tcl[-z]}
+tclp <- tcl/sum(tcl)
+
+
+
+rn <- dd[,1]
+dd <- dd[,-1]
+dd <- apply(dd,2, as.numeric)
+rownames(dd) <- rn
+
+
+
+library(ape)
+
+
+tree1 <- tree.cut1$tree.cl
+tree1 <- compute.brlen(tree1)
+tree1 <- as.hclust(tree1)
+
+
+
+dd <- t(dd)
+
+cc <- dd
+cc[which(dd <= (-3.84))] <- 1
+cc[which((dd > (-3.84)) & (dd < 3.84))] <- 2
+cc[which(dd >= 3.84)] <- 3
+library(RColorBrewer)
+#col <- brewer.pal(3, 'Reds')
+#col <- c('red', 'green', 'blue')
+col <- c('black', 'black', 'red')
+col <- c('white', 'white', 'blue')
+col <- col[cc]
+
+
+clod <- rev(as.numeric(tree.cut1$tree.cl$tip.label))
+
+heatmap(as.matrix(dd[as.numeric(tree.cut1$tree.cl$tip.label),]), Colv=NA, Rowv=as.dendrogram(tree1), col=col)
+
+png('cl_dates_homo.png', h=1000, w=2500)
+alphas <- seq(0,1, length.out=length(breaks))
+#par(mfrow=c(nrow(dd),1))
+par(mar=c(3,3,3,3))
+layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c(rep(nrow(dd)+2, nrow(dd)))),ncol=3), heights=tclp[clod], widths=c(0.05,0.92,0.03))
+par(mar=c(0,0,0,0))
+plot.phylo(tree.cut1$tree.cl,label.offset=0.1)
+for (i in clod) {
+ print(i)
+ par(mar=c(0,0,0,0))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+
+ #lcol[which(lcol <= 9)] <- 1
+
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ print(last.col)
+
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+#val2col(dd[i,], col=heat.colors(30)), border=NA)
+}
+plot.new()
+legend('right', as.character(lk), fill=last.col)
+
+dev.off()
+
+
+layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c(rep(nrow(dd)+2, nrow(dd)))),ncol=3), heights=tclp[clod], widths=c(0.05,0.92,0.03))
+par(mar=c(0,0,0,0))
+plot.phylo(tree.cut1$tree.cl,label.offset=0.1)
+ncol <- rainbow(nrow(dd))
+for (i in clod) {
+ print(i)
+ par(mar=c(0,0,0,0))
+ barplot(dd[i,], width=ptc, names.arg=FALSE, axes=FALSE, col=ncol[i])
+}
+
+
+
+
+vcol <- rainbow(nrow(dd))
+ncoli <- dd
+for (i in 1:nrow(dd)) {
+ lcol <- cut(dd[1,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ rlcol <- rank()
+ for (i in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[i])] <- i
+ }
+ lcol <- as.numeric(lcol)
+ for (j in 1:ncol(dd)) {
+ if (dd[i,j] < 3.84) {
+ ncoli[i,j] <- rgb(r=col2rgb(vcol[i])[1]/255, g=col2rgb(vcol[i])[2]/255, b=col2rgb(vcol[i])[3]/255, a=0.2)
+ } else {
+ ncoli[i,j] <- rgb(r=col2rgb(vcol[i])[1]/255, g=col2rgb(vcol[i])[2]/255, b=col2rgb(vcol[i])[3]/255, a=1)
+ }
+ }
+}
+
+barplot(t(ptt)[as.numeric(tree.cut1$tree.cl$tip.label),], col=rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)], width=ptc, las=3, space=0.05, cex.axis=0.7, border=NA)
+
+layout(matrix(c(1:nrow(ptt)), nrow=1), widths=ptc)
+od <- as.numeric(tree.cut1$tree.cl$tip.label)
+colod = rainbow(ncol(ptt))[od]
+for (i in 1:ncol(ptt)) {
+ par(mar=c(0,0,0,0))
+ barplot(as.matrix(ptt[i,od], ncol=1), col=colod, axes=FALSE)
+}
+
+k <- 1e-02
+lcol <- NULL
+lk <- k
+for (i in 1:5) {
+ lcol <- c(lcol, qchisq(1-k,1))
+ k <- k/10
+ lk <- c(lk,k)
+}
+lcol <- c(3.84, lcol)
+lcol <- c(-Inf,lcol)
+lcol <- c(lcol, Inf)
+lk <- c(0.05,lk)
+#lcol <- c(-rev(lcol), lcol)
+#lk <- c(-rev(lk), lk)
+#lcol <- c(min(dd), lcol)
+#lk <- c(1, lk)
+#breaks <- c(lcol, max(dd))
+breaks <- lcol
+
+lcol <- cut(dd[1,], breaks)
+ulcol <- names(table(lcol))
+lcol <- as.character(lcol)
+for (i in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[i])] <- i
+}
+lcol <- as.numeric(lcol)
+
+
+make.chi <- function(x) {
+ rs <- rowSums(x)
+ cs <- colSums(x)
+ n <- sum(x)
+
+}
+
+
+
+select.chi.classe <- function(tablechi, nb, active = TRUE) {
+ rowkeep <- NULL
+ if (active & !is.null(debsup)) {
+ print(debsup)
+ print('###############################################################@')
+ tablechi <- tablechi[1:(debsup-1),]
+ } else if (!active & !is.null(debsup)) {
+ tablechi <- tablechi[debsup:(debet-1),]
+ }
+ if (nb > nrow(tablechi)) {
+ nb <- nrow(tablechi)
+ }
+ for (i in 1:ncol(tablechi)) {
+ rowkeep <- append(rowkeep,order(tablechi[,i], decreasing = TRUE)[1:nb])
+ }
+ rowkeep <- unique(rowkeep)
+ rowkeep
+}
+
+
+plot.dendro.cloud <- function(tree, classes, chisqtable, nbbycl = 60, type.dendro = "phylogram", max.cex=2, min.cex=0.3, from.cmd = FALSE, bw = FALSE, lab = NULL, do.cloud=FALSE) {
+ library(wordcloud)
+ library(ape)
+ classes<-classes[classes!=0]
+ classes<-as.factor(classes)
+ sum.cl<-as.matrix(summary(classes, maxsum=1000000))
+ sum.cl<-(sum.cl/colSums(sum.cl)*100)
+ sum.cl<-round(sum.cl,2)
+ sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
+ sum.cl <- sum.cl[,1]
+ tree.order<- as.numeric(tree$tip.label)
+ vec.mat<-NULL
+
+ 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
+ }
+ if (!do.cloud) {
+ layout(matrix(vec.mat,length(sum.cl),2), heights=tclp[clod], widths=c(0.15,0.85))
+ } else {
+ row.keep <- select.chi.classe(chisqtable, nbbycl)
+ toplot <- chisqtable[row.keep,]
+ lclasses <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lclasses[[classe]] <- ntoplot
+ }
+ sup.keep <- select.chi.classe(chisqtable, nbbycl, active = FALSE)
+ toplot.sup <- chisqtable[debsup:(debet+1),]
+ toplot.sup <- toplot.sup[sup.keep, ]
+ lsup <- list()
+ for (classe in 1:length(sum.cl)) {
+ ntoplot <- toplot.sup[,classe]
+ ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+ ntoplot <- round(ntoplot, 0)
+ ntoplot <- ntoplot[1:nbbycl]
+ ntoplot <- ntoplot[order(ntoplot)]
+ #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+ lsup[[classe]] <- ntoplot
+ }
+ layout(matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1)),c((nrow(dd)+2):(2*nrow(dd)+1)), c((2*nrow(dd)+2):(3*nrow(dd)+1))),ncol=4), heights=tclp[clod], widths=c(0.05,0.05,0.05, 0.85))
+ }
+
+ if (! bw) {
+ col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ colcloud <- rainbow(length(sum.cl))
+ }
+ par(mar=c(0,0,0,0))
+ label.ori<-tree[[2]]
+ if (!is.null(lab)) {
+ tree$tip.label <- lab
+ } else {
+ tree[[2]]<-paste('classe ',tree[[2]])
+ }
+ plot.phylo(tree,label.offset=0.1,tip.col=col, type=type.dendro)
+ if (do.cloud) {
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(max.cex, min.cex), random.order=FALSE, colors = colcloud[i])
+ }
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,1,0),cex=0.9)
+ wordcloud(names(lsup[[i]]), lsup[[i]], scale = c(max.cex, min.cex), random.order=FALSE, colors = colcloud[i])
+ }
+ }
+
+ for (i in rev(tree.order)) {
+ par(mar=c(0,0,0,0))
+ lcol <- cut(dd[i,], breaks, include.lowest=TRUE)
+ ulcol <- names(table(lcol))
+ lcol <- as.character(lcol)
+ for (j in 1:length(ulcol)) {
+ lcol[which(lcol==ulcol[j])] <- j
+ }
+ lcol <- as.numeric(lcol)
+
+ #lcol[which(lcol <= 9)] <- 1
+
+ mcol <- rainbow(nrow(dd))[i]
+ last.col <- NULL
+ for (k in alphas) {
+ last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k))
+ }
+ print(last.col)
+
+ barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3))
+
+ }
+}
+
+
+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)
+ }
+ }
+}
+
+
+
+open_file_graph('cl_cloud_dates_gay.png', height=900, width=2500, svg=TRUE)
+plot.dendro.cloud(tree.cut1$tree.cl, classes, chistabletot, from.cmd=TRUE)
+
+dev.off()
projects / iramuteq / blobdiff