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$toplot
+ table.in <- table.out$toplot
notplot <- table.out$notplot
if (! is.null(notplot)) {
write.csv2(notplot, file = paste(filename, '_notplotted.csv', sep = ''))
isOverlaped <- FALSE
} else {
if(r>sqrt(.5)){
- print(paste(words[i], "could not be fit on page. It will not be plotted."))
- notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2]))
+ #print(paste(words[i], "could not be fit on page. It will not be plotted."))
+ notplot <- rbind(notplot,c(words[i], x[i,1], x[i,2], size[i], i))
isOverlaped <- FALSE
}
theta <- theta+thetaStep
}
}
}
+ nbnot <- nrow(notplot)
+ print(paste(nbnot, ' not plotted'))
row.names(toplot) <- words[toplot[,4]]
return(list(toplot = toplot, notplot = notplot))
}
return(toplot)
}
+new_tree_tot <- function(chd) {
+ lf <- chd$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
select.chi.classe <- function(tablechi, nb, active = TRUE) {
rowkeep <- NULL
if (active & !is.null(debsup)) {
- print(debsup)
- print('###############################################################@')
tablechi <- tablechi[1:(debsup-1),]
}
if (nb > nrow(tablechi)) {
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
tochange <- apply(rgbs, 2, is.yellow)
tochange <- which(tochange)
if (length(tochange)) {
- gr.col <- grey.colors(length(tochange), start = 0.5)
+ gr.col <- grey.colors(length(tochange), start = 0.5, end = 0.8)
}
compt <- 1
for (val in tochange) {
colors
}
-make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
+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
- }
- }
- 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(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))
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)) {
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[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))[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)
}
tree[[2]]<-paste('classe ',tree[[2]])
}
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$Nnode))
+ plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.5, y.lim=c(-0.3,tree$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=1.4)
+ 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]], 1.5, 2.5)
+ 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()
+ }
}
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),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)
}
#tree <- tree.cut1$tree.cl
#to.plot <- di
-plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, cmd=FALSE) {
+plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2), colbar=NULL, classes=NULL, direction = 'rightwards', cmd=FALSE) {
tree.order<- as.numeric(tree$tip.label)
if (!is.null(classes)) {
classes<-classes[classes!=0]
sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
}
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)
- } else {
- matlay <- matrix(c(1,2,3),1,byrow=TRUE)
- }
+ 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(3,0,2,0),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, 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))
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)]
}
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()
}
g <- graph.simi$graph
nodes <- data.frame(cbind(1:nrow(lo), V(g)$name))
colnames(nodes) <- c('id', 'label')
- print(nodes)
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 <- rep('red', nrow(lo))
+ col <- graph.simi$color
col <- t(sapply(col, col2rgb, alpha=TRUE))
- write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
+ write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo, size=graph.simi$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(grah.simi, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+
+
+graph.to.file <- function(graph.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]
+ 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$layout,-5,5,-5,5,-5,5)
+ print(layout)
+ V(g)$x <- layout[,1]
+ V(g)$y <- layout[,2]
+ if (ncol(layout) == 3) {
+ V(g)$z <- layout[,3]
}
if (community) {
member <- graph.simi$communities$membership
}
df <- get.data.frame(g, what='both')
if (!is.null(nodesfile)) {
- write.table(df$vertices, nodesfile, sep='\t')
+ write.table(df$vertices, nodesfile, sep='\t', row.names=FALSE)
+ }
+ if (!is.null(edgesfile)) {
+ write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
+ }
+ if (is.null(edgesfile) & is.null(nodesfile)) {
+ df
+ }
+}
+
+graph.to.file2 <- function(graph, layout, nodesfile = NULL, edgesfile = NULL, community = FALSE, color = NULL, sweight = NULL) {
+ require(igraph)
+ g <- graph
+ V(g)$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')
+ write.table(df$edges, edgesfile, sep='\t', row.names=FALSE)
}
if (is.null(edgesfile) & is.null(nodesfile)) {
df
}
}
+
projects / iramuteq / blobdiff