new graphics : not ready :)

[iramuteq] / Rscripts / Rgraph.R

diff --git a/Rscripts/Rgraph.R b/Rscripts/Rgraph.R
index ffbee4c..da03d5b 100644 (file)
--- a/Rscripts/Rgraph.R
+++ b/Rscripts/Rgraph.R
@@ -43,7 +43,7 @@ PlotDendroCut <- function(chd,filename,reso,clusternb) {
 #      dev.off()
 #}
 
 #      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=NUL) {
+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$colcoord)
        if (col) {
                if (what == 'coord') {
                        rowcoord <- as.matrix(afc$colcoord)


@@ -75,7 +75,7 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto
        if (!col) {
         classes <- as.matrix(apply(chitable,1,which.max))
         cex.par <- norm.vec(apply(chitable,1,max), 0.8,3)
        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, 60)
+        row.keep <- select.chi.classe(chitable, 80, active=active)

         rowcoord <- rowcoord[row.keep,]
         classes <- classes[row.keep]
         cex.par <- cex.par[row.keep]
         rowcoord <- rowcoord[row.keep,]
         classes <- classes[row.keep]
         cex.par <- cex.par[row.keep]


@@ -83,6 +83,15 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto
         classes <- 1:clnb
         cex.par <- rep(1,clnb)
     }
         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, ' -')
        #ntabtot <- cbind(rowcoord, classes)
        #if (!col) ntabtot <- ntabtot[row_keep,]
     xlab <- paste('facteur ', x, ' -')


@@ -94,15 +103,20 @@ PlotAfc2dCoul<- function(afc,chisqrtable,filename, what='coord',col=FALSE, axeto
 
        open_file_graph(filename, width = width, height = height)
        par(cex=PARCEX)
 
        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.in <- rowcoord[order(cex.par, decreasing = TRUE),]
     classes <- classes[order(cex.par, decreasing = TRUE)]
     cex.par <- cex.par[order(cex.par, decreasing = TRUE)]

-    table.in <- stopoverlap(table.in, cex.par=cex.par)
+    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))
     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) {
        #plot(rowcoord[,x],rowcoord[,y], pch='', xlab = xlab, ylab = ylab)
        #abline(h=0,v=0)
        #for (i in 1:clnb) {


@@ -128,7 +142,6 @@ open_file_graph <- function (filename, width=800, height = 800, quality = 100, s
             svg(filename.to.svg(filename), width=width, height=height)
         }
        } else {
             svg(filename.to.svg(filename), width=width, height=height)
         }
        } else {

-        #library(RSvgDevice)

         if (svg) {
             svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
         } else {
         if (svg) {
             svg(filename.to.svg(filename), width=width/74.97, height=height/74.97)
         } else {


@@ -173,7 +186,7 @@ overlap <- function(x1, y1, sw1, sh1, boxes) {
     .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
 }
 ########################################################
     .Call("is_overlap",x11,y11,sw11,sh11,boxes1)
 }
 ########################################################

-stopoverlap <- function(x, cex.par = NULL) {
+stopoverlap <- function(x, cex.par = NULL, xlim = NULL, ylim = NULL) {

 #from wordcloud
     library(wordcloud)
     tails <- "g|j|p|q|y"
 #from wordcloud
     library(wordcloud)
     tails <- "g|j|p|q|y"


@@ -182,9 +195,10 @@ stopoverlap <- function(x, cex.par = NULL) {
     thetaStep <- .1
     rStep <- .5
     toplot <- NULL
     thetaStep <- .1
     rStep <- .5
     toplot <- NULL

+    notplot <- NULL

 
 #    plot.new()
 
 #    plot.new()

-    plot(x[,1],x[,2], pch='')
+    plot(x[,1],x[,2], pch='', xlim = xlim, ylim = ylim)

 
     words <- rownames(x)
     if  (is.null(cex.par))  {
 
     words <- rownames(x)
     if  (is.null(cex.par))  {


@@ -202,8 +216,6 @@ stopoverlap <- function(x, cex.par = NULL) {
                y1<- x[i,2]
                wid <- strwidth(words[i],cex=size[i])
                ht <- strheight(words[i],cex=size[i])
                y1<- x[i,2]
                wid <- strwidth(words[i],cex=size[i])
                ht <- strheight(words[i],cex=size[i])

-           ht <- (ht + ht*.2) + .01
-        wid <- (wid + wid*.1) + .01

                isOverlaped <- TRUE
                while(isOverlaped){
                        if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&
                isOverlaped <- TRUE
                while(isOverlaped){
                        if(!overlap(x1-.5*wid,y1-.5*ht,wid,ht, boxes)) { #&&


@@ -215,6 +227,7 @@ stopoverlap <- function(x, cex.par = NULL) {
                        } else {
                                if(r>sqrt(.5)){
                                        print(paste(words[i], "could not be fit on page. It will not be plotted."))
                        } 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]))

                                        isOverlaped <- FALSE
                                }
                                theta <- theta+thetaStep
                                        isOverlaped <- FALSE
                                }
                                theta <- theta+thetaStep


@@ -225,7 +238,7 @@ stopoverlap <- function(x, cex.par = NULL) {
                }
     }
     row.names(toplot) <- words[toplot[,4]]
                }
     }
     row.names(toplot) <- words[toplot[,4]]

-    return(toplot)
+    return(list(toplot = toplot, notplot = notplot))

 }
 ###############################################################################
 
 }
 ###############################################################################
 


@@ -265,12 +278,12 @@ make_dendro_cut_tuple <- function(dendro_in, coordok, classeuce, x, nbt = 9) {
        dendro <- gsub('a','',dendro)
        dendro_tot_cl <- read.tree(text = dendro)
        #FIXME
        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 (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)
                dendro <- gsub(paste('\\(',0,',',0,'\\)',sep=''),0,dendro)
                for (cl in 1:clnb) {
                        dendro <- gsub(paste('\\(',0,',',cl,'\\)',sep=''),cl,dendro)


@@ -302,8 +315,13 @@ select_point_chi <- function(tablechi, chi_limit) {
        row_keep
 }
 
        row_keep
 }
 

-select.chi.classe <- function(tablechi, nb) {
+select.chi.classe <- function(tablechi, nb, active = TRUE) {

     rowkeep <- NULL
     rowkeep <- NULL

+    if (active & !is.null(debsup)) {
+        print(debsup)
+        print('###############################################################@')
+        tablechi <- tablechi[1:(debsup-1),]
+    }

     if (nb > nrow(tablechi)) {
         nb <- nrow(tablechi)
     }
     if (nb > nrow(tablechi)) {
         nb <- nrow(tablechi)
     }


@@ -427,14 +445,32 @@ create_afc_table <- function(x) {
        res
 }
 
        res
 }
 

-make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, leg = FALSE, cmd = FALSE, black = FALSE, xminmax=NULL, yminmax=NULL) {
-    if (is.null(xminmax)) {
-        xminmax <- c(min(toplot[,1]) + (0.1 * min(toplot[,1])), max(toplot[,1]) + (0.1 * max(toplot[,1])))
+is.yellow <- function(my.color) {
+    if ((my.color[1] > 200) & (my.color[2] > 200) & (my.color[3] < 20)) {
+        return(TRUE)
+    } else {
+        return(FALSE)

     }
     }

-    if (is.null(yminmax)) {
-        yminmax <- c(min(toplot[,2]) + (0.1 * min(toplot[,2])), max(toplot[,2]) + (0.1 * max(toplot[,2])))
+}
+
+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))

     }
     }

-       rain <- rainbow(clnb)
+    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) {
+    
+    rain <- rainbow(clnb)

     compt <- 1
     tochange <- NULL
     for (my.color in rain) {
     compt <- 1
     tochange <- NULL
     for (my.color in rain) {


@@ -468,18 +504,131 @@ make_afc_graph <- function(toplot, classes, clnb, xlab, ylab, cex.txt = NULL, le
     }
 }
 
     }
 }
 

+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$tip.label)
+       vec.mat<-NULL
+    row.keep <- select.chi.classe(chisqtable, nbbycl)
+    toplot <- chisqtable[row.keep,]
+    lclasses <- list()
+    for (classe in 1:length(sum.cl)) {
+       ntoplot <- toplot[,classe]
+       names(ntoplot) <- rownames(toplot)
+       ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+       ntoplot <- round(ntoplot, 0)
+       ntoplot <- ntoplot[1:nbbycl]
+       #ntoplot <- ntoplot[order(ntoplot)]
+       #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+       lclasses[[classe]] <- ntoplot
+    }
+    vec.mat <- matrix(1, nrow = 3, ncol = length(sum.cl))
+       vec.mat[2,] <- 2
+    vec.mat[3,] <- 3:(length(sum.cl)+2)
+    layout(matrix(vec.mat, nrow=3, ncol=length(sum.cl)),heights=c(1,1,6))
+    if (! bw) {
+        col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+        col <- del.yellow(col)
+        colcloud <- rainbow(length(sum.cl))
+        colcloud <- del.yellow(colcloud)
+    }
+    label.ori<-tree[[2]]
+    if (!is.null(lab)) {
+        tree$tip.label <- lab
+    } else {
+           tree[[2]]<-paste('classe ',tree[[2]])
+    }
+       par(mar=c(1,1,0,1))
+       plot.phylo(tree,label.offset=0, tip.col=col, type=type.dendro, direction = 'downwards', srt=90, adj = 0.5, cex = 1.4, y.lim=c(-0.3,tree$Nnode))
+       par(mar=c(0,0,0,0))
+       d <- barplot(-sum.cl[tree.order], col=col, names.arg='', axes=FALSE, axisname=FALSE)
+       text(x=d, y=(-sum.cl[tree.order]+3), label=paste(round(sum.cl[tree.order],1),'%'), cex=1.4)
+    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)
+        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)
+        }
+    }
+    
+}
+
+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$tip.label)
+       vec.mat<-NULL
+    row.keep <- select.chi.classe(chisqtable, nbbycl)
+    toplot <- chisqtable[row.keep,]
+    lclasses <- list()
+    for (classe in 1:length(sum.cl)) {
+       ntoplot <- toplot[,classe]
+       ntoplot <- ntoplot[order(ntoplot, decreasing = TRUE)]
+       ntoplot <- round(ntoplot, 0)
+       ntoplot <- ntoplot[1:nbbycl]
+       ntoplot <- ntoplot[order(ntoplot)]
+       #ntoplot <- ifelse(length(ntoplot) > nbbycl, ntoplot[1:nbbycl], ntoplot)
+       lclasses[[classe]] <- ntoplot
+    }
+       for (i in 1:length(sum.cl)) vec.mat<-append(vec.mat,1)
+       v<-2
+       for (i in 1:length(sum.cl)) {
+               vec.mat<-append(vec.mat,v)
+               v<-v+1
+       }    
+    layout(matrix(vec.mat,length(sum.cl),2),widths=c(1,2))
+    if (! bw) {
+        col <- rainbow(length(sum.cl))[as.numeric(tree$tip.label)]
+        colcloud <- rainbow(length(sum.cl))
+    }
+    par(mar=c(0,0,0,0))
+    label.ori<-tree[[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)
+    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])
+    }
+}
+

 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)
 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$tip.label)
        sum.cl<-(sum.cl/colSums(sum.cl)*100)
        sum.cl<-round(sum.cl,2)
        sum.cl<-cbind(sum.cl,as.matrix(100-sum.cl[,1]))
     tree.order<- as.numeric(tree$tip.label)

+
+

     if (! bw) {
     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.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.vec<-rainbow(nrow(sum.cl))[as.numeric(tree[[2]])]
     } else {
         col = 'black'


@@ -531,10 +680,24 @@ plot.dendropr <- function(tree, classes, type.dendro="phylogram", histo=FALSE, f
 }
 #tree <- tree.cut1$tree.cl
 #to.plot <- di
 }
 #tree <- tree.cut1$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, cmd=FALSE) {

     tree.order<- as.numeric(tree$tip.label)
     tree.order<- as.numeric(tree$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))
     par(mar=c(0,0,0,0))

-    layout(matrix(c(1,2,3),1,byrow=TRUE), widths=lay.width,TRUE)
+       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)
+       }
+    layout(matlay, widths=lay.width,TRUE)

        par(mar=c(3,0,2,0),cex=1)
        label.ori<-tree[[2]]
     if (!is.null(lab)) {
        par(mar=c(3,0,2,0),cex=1)
        label.ori<-tree[[2]]
     if (!is.null(lab)) {


@@ -544,15 +707,27 @@ plot.dendro.lex <- function(tree, to.plot, bw=FALSE, lab=NULL, lay.width=c(3,3,2
     }
     to.plot <- matrix(to.plot[,tree.order], nrow=nrow(to.plot), dimnames=list(rownames(to.plot), colnames(to.plot)))
     if (!bw) {
     }
     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)
     } 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)

-    
+       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)
     c <- colMeans(d)
     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)
     c <- colMeans(d)


@@ -714,3 +889,95 @@ 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)
 
 #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')
+       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 <- t(sapply(col, col2rgb, alpha=TRUE))
+       write.gexf(nodes, edges, output=fileout, nodesAtt=nodesatt, nodesVizAtt=list(color=col,position=lo))
+}