}
###############################################################################
+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)<rot.per
+ r <-0
+ theta <- runif(1,0,2*pi)
+ x1<-.5
+ y1<-.5
+ wid <- strwidth(words[i],cex=size[i],...)
+ ht <- strheight(words[i],cex=size[i],...)
+ #mind your ps and qs
+ if(grepl(tails,words[i]))
+ ht <- ht + ht*.2
+ if(rotWord){
+ tmp <- ht
+ ht <- wid
+ wid <- tmp
+ }
+ isOverlaped <- TRUE
+ while(isOverlaped){
+ if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht) &&
+ x1-.5*wid>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)
+}
+
make_tree_tot <- function (chd) {
library(ape)
lf<-chd$list_fille
tochange <- apply(rgbs, 2, is.yellow)
tochange <- which(tochange)
if (length(tochange)) {
- gr.col <- grey.colors(length(tochange))
+ gr.col <- grey.colors(length(tochange), start = 0.5, end = 0.8)
}
compt <- 1
for (val in tochange) {
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
- }
- }
- cl.color <- rain[classes]
+ #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(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) {
names(ntoplot) <- rownames(toplot)
ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
ntoplot <- round(ntoplot, 0)
- ntoplot <- ntoplot[1:nbbycl]
+ 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(1,1,6))
+ layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(2,1,6))
if (! bw) {
- col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+ col <- rainbow(length(sum.cl))
col <- del.yellow(col)
+ col <- col[as.numeric(tree$tip.label)]
colcloud <- rainbow(length(sum.cl))
colcloud <- del.yellow(colcloud)
}
} else {
tree[[2]]<-paste('classe ',tree[[2]])
}
- par(mar=c(1,1,0,1))
+ par(mar=c(2,1,0,1))
plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
par(mar=c(0,0,0,0))
d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)
#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]], 1.5, 2.5)
+ vcex <- norm.vec(lclasses[[i]], 1, 2)
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()
+ }
}
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)
- ntoplot <- ntoplot[1:nbbycl]
+ 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
}
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(4, 0.8), random.order=FALSE, colors = colcloud[i])
+ wordcloud(names(lclasses[[i]]), lclasses[[i]], scale = c(2.5, 0.5), random.order=FALSE, colors = colcloud[i])
}
}
par(mar=c(0,0,0,0))
if (!is.null(classes)) {
matlay <- matrix(c(1,2,3,4),1,byrow=TRUE)
- lay.width <- c(3,1,3,2)
+ lay.width <- c(3,2,3,2)
} else {
matlay <- matrix(c(1,2,3),1,byrow=TRUE)
}
layout(matlay, widths=lay.width,TRUE)
- par(mar=c(3,0,2,0),cex=1)
+ par(mar=c(3,0,2,4),cex=1)
label.ori<-tree[[2]]
if (!is.null(lab)) {
- tree$tip.label <- lab
+ tree$tip.label <- lab[tree.order]
} else {
tree[[2]]<-paste('classe ',tree[[2]])
}
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)
if (!is.null(classes)) {
par(cex=0.7)
par(mar=c(3,0,2,1))
col <- t(sapply(col, col2rgb, alpha=TRUE))
write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
}
+
+
+graph.to.file <- function(grah.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+ require(igraph)
+ g <- graph.simi$graph
+ V(g)$weight <- graph.simi$eff
+ V(g)$x <- graph.simi$layout[,1]
+ V(g)$y <- graph.simi$layout[,2]
+ if (ncol(graph.simi$layout) == 3) {
+ V(g)$z <- graph.simi$layout[,3]
+ }
+ 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')
+ }
+ if (!is.null(edgesfile)) {
+ write.table(df$edges, edgesfile, sep='\t')
+ }
+ if (is.null(edgesfile) & is.null(nodesfile)) {
+ df
+ }
+}
projects / iramuteq / blobdiff