X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=0673aa491013f6a0381bacf5ae846d43e943aa5e;hp=579bcae43cd507fa2219c499cd32961919459bb7;hb=bf4bf75287ff2a34d072cf7f7c0dea6ba4281a24;hpb=8d5fdf0146b7b3b1898bed4824abee96b270b33d

diff --git a/PrintRScript.py b/PrintRScript.py
old mode 100644
new mode 100755
index 579bcae..0673aa4
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -13,17 +13,21 @@ import logging
 log = logging.getLogger('iramuteq.printRscript')
 
 class PrintRScript :
-    def __init__ (self, analyse):
+    def __init__ (self, analyse, parametres = None):
         log.info('Rscript')
         self.pathout = analyse.pathout
         self.analyse = analyse
-        self.parametres = analyse.parametres
-        self.scriptout = self.pathout['lastRscript.R']
+        if parametres is None :
+            self.parametres = analyse.parametres
+        else :
+            self.parametres = parametres
+        #self.scriptout = ffr(self.pathout['lastRscript.R'])
+        self.scriptout = self.pathout['temp']
         self.script =  u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
-    
+
     def add(self, txt) :
         self.script = '\n'.join([self.script, txt])
-    
+
     def defvar(self, name, value) :
         self.add(' <- '.join([name, value]))
 
@@ -109,7 +113,7 @@ class Alceste2(PrintRScript) :
 #
 
 
-def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False):
+def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False, nbproc=1):
     txt = """
     source("%s")
     source("%s")
@@ -154,7 +158,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     data1 <- as(data1, "dgCMatrix")
     row.names(data1) <- 1:nrow(data1)
     """ % ffr(DicoPath['TableUc1'])
-    
+
     if classif_mode == 0:
         txt += """
         data2 <- readMM("%s")
@@ -163,29 +167,34 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         """ % ffr(DicoPath['TableUc2'])
     txt += """
     log1 <- "%s"
-    chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, log.file = log1)
-    """ % ffr(DicoPath['log-chd1.txt'])
-    
+    print('FIXME : source newCHD')
+    source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R')
+    nbproc <- %s
+    chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', select.next='size', sample=20, amp=500, proc.nb=nbproc)
+    #chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log1)
+    """ % (ffr(DicoPath['log-chd1.txt']), nbproc)
+
     if classif_mode == 0:
         txt += """
     log2 <- "%s"
-    chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, log.file = log2)
+    chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method =
+    svd.method, libsvdc.path = libsvdc.path)#, log.file = log2)
     """ % ffr(DicoPath['log-chd2.txt'])
-    
+
     txt += """
     #lecture des uce
     listuce1<-read.csv2("%s")
     """ % ffr(DicoPath['listeuce1'])
-    
+
     if classif_mode == 0:
         txt += """
         listuce2<-read.csv2("%s")
         """ % ffr(DicoPath['listeuce2'])
-        
+
     txt += """
     rm(data1)
     """
-    
+
     if classif_mode == 0:
         txt += """
         rm(data2)
@@ -193,26 +202,34 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     txt += """
     classif_mode <- %i
     mincl <- %i
+    if (mincl == 0) {mincl <- round(nrow(chd1$n1)/(nbt+1))}
     uceout <- "%s"
+    write.csv2(chd1$n1, file="%s")
     if (classif_mode == 0) {
         chd.result <- Rchdtxt(uceout, chd1, chd2 = chd2, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+        classeuce1 <- chd.result$cuce1
+        tree.tot1 <- make_tree_tot(chd1)
+        tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
+
     } else {
-        chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+        #chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+        tree.tot1 <- make_tree_tot(chd1)
+        terminales <- find.terminales(chd1$n1, chd1$list_mere, chd1$list_fille, mincl)
+        tree.cut1 <- make.classes(terminales, chd1$n1, tree.tot1$tree.cl, chd1$list_fille)
+        write.csv2(tree.cut1$n1, uceout)
+        chd.result <- tree.cut1
     }
-    n1 <- chd.result$n1
-    classeuce1 <- chd.result$cuce1
-    classes<-n1[,ncol(n1)]
-    write.csv2(n1, file="%s")
-    rm(n1)
-    """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv']))
-    
+    classes<-chd.result$n1[,ncol(chd.result$n1)]
+    write.csv2(chd.result$n1, file="%s")
+    """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1-1.csv']), ffr(DicoPath['n1.csv']))
+
     txt += """
-    tree.tot1 <- make_tree_tot(chd1)
+#    tree.tot1 <- make_tree_tot(chd1)
 #    open_file_graph("%s", widt = 600, height=400)
 #    plot(tree.tot1$tree.cl)
 #    dev.off()
     """ % ffr(DicoPath['arbre1'])
-    
+
     if classif_mode == 0:
         txt += """
         classeuce2 <- chd.result$cuce2
@@ -220,19 +237,18 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
 #        open_file_graph("%s", width = 600, height=400)
 #        plot(tree.tot2$tree.cl)
 #        dev.off()
-        """ % ffr(DicoPath['arbre2'] ) 
-              
+        """ % ffr(DicoPath['arbre2'] )
+
     txt += """
-    tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
-    save(tree.cut1, file="%s")
-    
+        save(tree.cut1, file="%s")
+
     open_file_graph("%s", width = 600, height=400)
     plot.dendropr(tree.cut1$tree.cl,classes, histo=TRUE)
     open_file_graph("%s", width = 600, height=400)
     plot(tree.cut1$dendro_tot_cl)
     dev.off()
     """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']), ffr(DicoPath['arbre1']))
-    
+
     if classif_mode == 0:
         txt += """
         tree.cut2 <- make_dendro_cut_tuple(tree.tot2$dendro_tuple, chd.result$coord_ok, classeuce2, 2, nbt)
@@ -243,12 +259,12 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         plot(tree.cut2$dendro_tot_cl)
         dev.off()
         """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
-        
+
     txt += """
-    
+
     #save.image(file="%s")
     """ % (ffr(DicoPath['RData']))
-    
+
     fileout = open(DicoPath['Rchdtxt'], 'w')
     fileout.write(txt)
     fileout.close()
@@ -334,9 +350,14 @@ datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1,
 dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
 """ % (ffr(DictChdTxtOut['Contout']), ffr(DictChdTxtOut['ContSupOut']), ffr(DictChdTxtOut['ContEtOut']))
     txt += """
-tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
-tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
-tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
+print('ATTENTION NEW BUILD PROF')
+#tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
+#tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
+#tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
+tablesqrpact<-new.build.prof(as.matrix(dataact),n1,clnb)
+tablesqrpsup<-new.build.prof(as.matrix(datasup),n1,clnb)
+tablesqrpet<-new.build.prof(as.matrix(dataet),n1,clnb)
+
 """
     txt += """
 PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
@@ -447,12 +468,20 @@ def write_afc_graph(self):
     if self.param['svg'] : svg = 'TRUE'
     else : svg = 'FALSE'
 
+    if self.param['typegraph'] == 4 :
+        nodesfile = os.path.join(os.path.dirname(self.fileout),'nodes.csv')
+        edgesfile = os.path.join(os.path.dirname(self.fileout),'edges.csv')
+    else :
+        nodesfile = 'NULL'
+        edgesfile = 'NULL'
+
     with open(self.RscriptsPath['afc_graph'], 'r') as f:
         txt = f.read()
 
 #    self.DictPathOut['RData'], \
     scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\
     self.param['typegraph'], \
+    edgesfile, nodesfile, \
     self.param['what'], \
     self.param['facteur'][0],\
     self.param['facteur'][1], \
@@ -589,7 +618,7 @@ def barplot(table, parametres, intxt = False) :
             height <- %i
             open_file_graph("%s",width = width, height = height, svg = %s)
         	par(mar=c(0,0,0,0))
-    	    layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
+    	    layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(12)))
             par(mar=c(8,4,1,0))
             yp = ifelse(length(toinf), 0.2, 0)
             ym = ifelse(length(tominf), 0.2, 0)
@@ -720,10 +749,11 @@ class PrintSimiScript(PrintRScript) :
             else :
                 txt += """
                 word <- FALSE
+                index <- NULL
                 """
             txt += """
             dm <-readMM(dm.path)
-            cn <- read.table(cn.path, sep='\t', quote='"')
+            cn <- read.table(cn.path, sep="\t", quote='"')
             colnames(dm) <- cn[,1]
             if (file.exists(selected.col)) {
                 sel.col <- read.csv2(selected.col, header = FALSE)
@@ -780,7 +810,7 @@ class PrintSimiScript(PrintRScript) :
             txt += """
             load("%s")
             """ % ffr(self.pathout['RData.RData'])
-        
+
         if self.parametres['coeff'] == 0 :
             method = 'cooc'
             if not self.parametres['keep_coord'] :
@@ -788,6 +818,13 @@ class PrintSimiScript(PrintRScript) :
                 method <- 'cooc'
                 mat <- make.a(dm)
                 """
+        elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard' :
+            method = 'Jaccard'
+            if not self.parametres['keep_coord'] :
+                txt += """
+                method <- 'Jaccard'
+                mat <- sparse.jaccard(dm)
+                """
         else :
             if not self.parametres['keep_coord'] :
                 txt += """
@@ -806,7 +843,7 @@ class PrintSimiScript(PrintRScript) :
                 method <- 'binomial'
                 mat <- binom.sim(dm)
                 """
-        elif self.parametres['coeff'] != 0 :
+        elif self.parametres['coeff'] != 0 and self.analyse.indices[self.parametres['coeff']] != 'Jaccard':
             method = self.analyse.indices[self.parametres['coeff']]
             if not self.parametres['keep_coord'] :
                 txt += """
@@ -844,10 +881,13 @@ class PrintSimiScript(PrintRScript) :
             txt += """
             mat <- graph.word(mat, index)
             cs <- colSums(mat)
-            if (length(cs)) mat <- mat[,-which(cs==0)]
+            if (length(which(cs==0))) mat <- mat[,-which(cs==0)]
             rs <- rowSums(mat)
-            if (length(rs)) mat <- mat[-which(rs==0),]
-            if (length(cs)) dm <- dm[, -which(cs==0)]
+            if (length(which(rs==0))) mat <- mat[-which(rs==0),]
+            if (length(which(cs==0))) dm <- dm[,-which(cs==0)]
+            if (word) {
+                index <- which(colnames(mat)==forme)
+            }
             """
 
         if self.parametres['layout'] == 0 : layout = 'random'
@@ -855,6 +895,8 @@ class PrintSimiScript(PrintRScript) :
         if self.parametres['layout'] == 2 : layout = 'frutch'
         if self.parametres['layout'] == 3 : layout = 'kawa'
         if self.parametres['layout'] == 4 : layout = 'graphopt'
+        if self.parametres['layout'] == 5 : layout = 'spirale'
+        if self.parametres['layout'] == 6 : layout = 'spirale3D'
 
 
         self.filename=''
@@ -874,7 +916,7 @@ class PrintSimiScript(PrintRScript) :
             while os.path.exists(os.path.join(dirout,'web_'+str(graphnb))):
                 graphnb +=1
             self.filename = ffr(os.path.join(dirout,'web_'+str(graphnb)))
-            os.mkdir(self.filename)        
+            os.mkdir(self.filename)
             self.filename = os.path.join(self.filename, 'gexf.gexf')
         if self.parametres['type_graph'] == 4 : 
             graphnb = 1
@@ -937,7 +979,7 @@ class PrintSimiScript(PrintRScript) :
         if self.parametres['film'] : 
             txt += """
             film <- "%s"
-            """ % self.pathout['film']
+            """ % ffr(self.pathout['film'])
         else : 
             txt += """
             film <- NULL
@@ -1061,7 +1103,7 @@ class PrintSimiScript(PrintRScript) :
         txt += """
         eff <- colSums(dm)
         x <- list(mat = mat, eff = eff)
-        graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo)
+        graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo, index.word=index)
         """ % (method, type, layout, arbremax, coeff_tv, coeff_te)
             
         if self.parametres.get('bystar',False) :
@@ -1124,6 +1166,17 @@ class PrintSimiScript(PrintRScript) :
         """ % svg
         txt += """
         vertex.col <- cols
+        col.from.proto <- F
+        if (col.from.proto) {
+            proto.col <- read.table('/tmp/matcol.csv')
+            v.proto.names <- make.names(proto.col[,1])
+            v.proto.col <- as.character(proto.col[,2])
+            v.proto.col[which(v.proto.col=='black')] <- 'yellow'
+            v.names <- V(graph.simi$graph)$name
+            num.color <- sapply(v.names, function(x) {if (x %%in%% v.proto.names) {v.proto.col[which(v.proto.names==x)]} else {'pink'}})
+            vertex.col <- num.color
+            V(graph.simi$graph)$proto.color <- vertex.col
+        }
         if (!is.null(graph.simi$com)) {
             com <- graph.simi$com
             colm <- rainbow(length(com))
@@ -1134,6 +1187,12 @@ class PrintSimiScript(PrintRScript) :
                 vertex.label.color <- colm[membership(com)]
             }
         }
+        if (!length(graph.simi$elim)==0) {
+            vertex.label.color <- vertex.label.color[-graph.simi$elim]
+            if (length(label.cex > 1)) {
+                 label.cex <- label.cex[-graph.simi$elim]
+            }
+        }
         coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = vertex.col, vertex.label.color = vertex.label.color, vertex.label.cex=label.cex, vertex.size = vertex.size, edge.col = cola, leg=leg, width = width, height = height, alpha = alpha, movie = film, edge.curved = edge.curved, svg = svg)
         save.image(file="%s")
         """ % (type, self.filename, ffr(self.pathout['RData']))
@@ -1189,7 +1248,7 @@ class ProtoScript(PrintRScript) :
         }
         mat <- read.csv2("%s", header = FALSE, row.names=1, sep='\t', quote='"', dec='.')
         open_file_graph("%s",height=800, width=1000)
-        prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s')
+        prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s', mat.col.path='/tmp/matcol.csv')
         dev.off()
         """ % (ffr(self.analyse.pathout['table.csv']), ffr(self.analyse.pathout['proto.png']), self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
         self.add(txt)
@@ -1204,15 +1263,16 @@ class ExportAfc(PrintRScript) :
         """
 
 class MergeGraphes(PrintRScript) :
-    def __init__(self, parametres):
+    def __init__(self, analyse):
         self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
         self.pathout = PathOut()
-        self.parametres = parametres
+        self.parametres = analyse.parametres
         self.scriptout = self.pathout['temp']
-        
+        self.analyse = analyse 
+
     def make_script(self) :
         #FIXME
-        
+
         txt = """
         library(igraph)
         library(Matrix)
@@ -1224,7 +1284,7 @@ class MergeGraphes(PrintRScript) :
         V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100
         graphs[['%s']] <- g
         """
-        for i, graph in enumerate(self.parametres['lgraphes']) :
+        for i, graph in enumerate(self.parametres['graphs']) :
             path = os.path.dirname(graph)
             gname = ''.join(['g', `i`])
             RData = os.path.join(path,'RData.RData')
@@ -1232,7 +1292,12 @@ class MergeGraphes(PrintRScript) :
         self.add(txt)
         self.sources([self.analyse.parent.RscriptsPath['simi']])
         txt = """
-        ng <- merge.graph(graphs)
+        merge.type <- 'proto'
+        if (merge.type == 'normal') {
+            ng <- merge.graph(graphs)
+        } else {
+            ng <- merge.graph.proto(graphs)
+        }
         ngraph <- list(graph=ng, layout=layout.fruchterman.reingold(ng, dim=3), labex.cex=V(ng)$weight)
         write.graph(ng, "%s", format = 'graphml')
         """ % ffr(self.parametres['grapheout'])
@@ -1304,4 +1369,335 @@ class FreqMultiScript(PrintRScript):
         dev.off()
         """ % ffr(self.pathout['barplotrow.png'])
         self.add(txt)
-        self.write()  
+        self.write()
+
+class LabbeScript(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['distance-labbe.R'],
+                      self.analyse.parent.RscriptsPath['Rgraph']])
+        txt = """
+        tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1)
+        """ % (ffr(self.pathout['tableafcm.csv']))
+        txt += """
+        dist.mat <- dist.labbe(tab)
+        dist.mat <- as.dist(dist.mat, upper=F, diag=F)
+        write.table(as.matrix(dist.mat), "%s", sep='\t')
+        library(cluster)
+        library(ape)
+        chd <- hclust(dist.mat, method="ward.D2")
+        open_file_graph("%s", width=1000, height=1000, svg=F)
+        par(cex=1.2)
+        plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
+        dev.off()
+        """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png']))
+        txt +="""
+        open_file_graph("%s", width=1000, height=1000, svg=F)
+        par(mar=c(10,1,1,10))
+        heatmap(as.matrix(dist.mat), symm = T, distfun=function(x) as.dist(x), margins=c(10,10))
+        dev.off()
+        """ % ffr(self.pathout['labbe-heatmap.png'])
+        txt += """
+        #http://stackoverflow.com/questions/3081066/what-techniques-exists-in-r-to-visualize-a-distance-matrix
+        dst <- data.matrix(dist.mat)
+        dim <- ncol(dst)
+        rn <- row.names(as.matrix(dist.mat))
+        open_file_graph("%s", width=1500, height=1000, svg=F)
+        par(mar=c(10,10,3,3))
+        image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="", col=heat.colors(99), breaks=seq(0.01,1,0.01))
+        axis(1, 1:dim, rn, cex.axis = 0.9, las=3)
+        axis(2, 1:dim, rn, cex.axis = 0.9, las=1)
+        text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6)
+        dev.off()
+        """  % ffr(self.pathout['labbe-matrix.png'])
+        txt += """
+        library(igraph)
+        g <- graph.adjacency(as.matrix(1-dist.mat), mode="lower", weighted=T)
+        write.graph(g, file="%s", format='graphml')
+        open_file_graph("%s", width=1000, height=1000, svg=F)
+        plot(g)
+        dev.off()
+        E(g)$weight <- 1 - E(g)$weight
+        g <- minimum.spanning.tree(g)
+        E(g)$weight <- 1 - E(g)$weight
+        write.graph(g, file="%s", format='graphml')
+        open_file_graph("%s", width=1000, height=1000, svg=F)
+        plot(g)
+        dev.off()
+        """ % (ffr(self.pathout['graph_tot.graphml']), ffr(self.pathout['graph_tot.png']), ffr(self.pathout['graph_min.graphml']), ffr(self.pathout['graph_min.png']))
+        self.add(txt)
+        self.write()
+
+class ChronoChi2Script(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+        print self.parametres
+        txt = """
+        inRData <- "%s"
+        dendrof <- "%s"
+        load(inRData)
+        load(dendrof)
+        """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+        txt += """
+        svg <- %s
+        """ % self.parametres['svg']
+        txt += """
+        tc <- which(grepl("%s",rownames(chistabletot)))
+        rn <- rownames(chistabletot)[tc]
+        tc <- tc[order(rn)]
+        dpt <- chistabletot[tc,]
+        tot <- afctable[tc,]
+        tcp <- rowSums(tot)
+        ptc <- tcp/sum(tcp)
+        dpt <- t(dpt)
+        dd <- dpt
+        """ % self.parametres['var'].replace(u'*', u"\\\\*")
+        txt += """
+        classes <- n1[,ncol(n1)]
+        tcl <- table(classes)
+        if ('0' %in% names(tcl)) {
+            to.vire <- which(names(tcl) == '0')
+            tcl <- tcl[-to.vire]
+        }
+        tclp <- tcl/sum(tcl)
+
+        #chi2 colors
+        library(ape)
+        k <- 1e-02
+        lcol <- NULL
+        lk <- k
+        for (i in 1:5) {
+            lcol <- c(lcol, qchisq(1-k,1))
+            k <- k/10
+            lk <- c(lk,k)
+        }
+        lcol <- c(3.84, lcol)
+        lcol <- c(-Inf,lcol)
+        lcol <- c(lcol, Inf)
+        lk <- c(0.05,lk)
+        breaks <- lcol
+        alphas <- seq(0,1, length.out=length(breaks))
+        clod <- rev(as.numeric(tree.cut1$tree.cl$tip.label))
+        #end
+        """
+        txt += """
+        open_file_graph("%s", w=%i, h=%i, svg=svg)
+        """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+        txt += """
+        par(mar=c(3,3,3,3))
+        mat.graphic <- matrix(c(rep(1,nrow(dd)),c(2:(nrow(dd)+1))), ncol=2)
+        mat.graphic <- rbind(mat.graphic, c(max(mat.graphic) + 1 , max(mat.graphic) + 2))
+        hauteur <- tclp[clod] * 0.9
+        heights.graphic <- append(hauteur, 0.1)
+        layout(mat.graphic, heights=heights.graphic, widths=c(0.15,0.85))
+        par(mar=c(0,0,0,0))
+        tree.toplot <- tree.cut1$tree.cl
+        num.label <- as.numeric(tree.cut1$tree.cl$tip.label)
+        col.tree <- rainbow(length(num.label))[num.label]
+        #tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
+        plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T, tip.color = col.tree)
+        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)
+            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))
+        }
+        plot(0,type='n',axes=FALSE,ann=FALSE)
+        label.coords <- barplot(rep(1, ncol(dd)), width=ptc, names.arg = F, las=2, axes=F, ylim=c(0,1), plot=T, col='white')
+        text(x=label.coords, y=0.5, labels=rn[order(rn)], srt=90)
+        dev.off()
+        """
+        self.add(txt)
+        self.write()
+
+class ChronoPropScript(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+        print self.parametres
+        txt = """
+        inRData <- "%s"
+        dendrof <- "%s"
+        load(inRData)
+        load(dendrof)
+        """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+        txt += """
+        svg <- %s
+        """ % self.parametres['svg']
+        txt += """
+        tc <- which(grepl("%s",rownames(chistabletot)))
+        rn <- rownames(chistabletot)[tc]
+        tc <- tc[order(rn)]
+        dpt <- chistabletot[tc,]
+        tot <- afctable[tc,]
+        tcp <- rowSums(tot)
+        ptc <- tcp/sum(tcp)
+        dpt <- t(dpt)
+        dd <- dpt
+        """ % self.parametres['var'].replace(u'*', u"\\\\*")
+        txt += """
+        classes <- n1[,ncol(n1)]
+        tcl <- table(classes)
+        if ('0' %in% names(tcl)) {
+            to.vire <- which(names(tcl) == '0')
+            tcl <- tcl[-to.vire]
+        }
+        tclp <- tcl/sum(tcl)
+        """
+        txt += """
+        open_file_graph("%s", w=%i, h=%i, svg=svg)
+        """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+        txt+= """
+        ptt <- prop.table(as.matrix(tot), 1)
+        par(mar=c(10,2,2,2))
+        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)
+        dev.off()
+        """
+        self.add(txt)
+        self.write()
+
+class ChronoggScript(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+        print self.parametres
+        txt = """
+        library(ggplot2)
+        inRData <- "%s"
+        dendrof <- "%s"
+        load(inRData)
+        load(dendrof)
+        """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+        txt += """
+        svg <- %s
+        """ % self.parametres['svg']
+        txt += """
+        tc <- which(grepl("%s",rownames(chistabletot)))
+        rn <- rownames(chistabletot)[tc]
+        tc <- tc[order(rn)]
+        dpt <- chistabletot[tc,]
+        tot <- afctable[tc,]
+        tcp <- rowSums(tot)
+        ptc <- tcp/sum(tcp)
+        dpt <- t(dpt)
+        dd <- dpt
+        """ % self.parametres['var'].replace(u'*', u"\\\\*")
+        txt += """
+        classes <- n1[,ncol(n1)]
+        tcl <- table(classes)
+        if ('0' %in% names(tcl)) {
+            to.vire <- which(names(tcl) == '0')
+            tcl <- tcl[-to.vire]
+        }
+        tclp <- tcl/sum(tcl)
+        ptt <- prop.table(as.matrix(tot), 1)
+        ptt <- ptt[,as.numeric(tree.cut1$tree.cl$tip.label)]
+        rownames(ptt) <- cumsum(ptc)
+        nptt<-as.data.frame(as.table(ptt))
+        nptt[,1]<-as.numeric(as.character(nptt[,1]))
+        col <- rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)]
+        """
+        txt += """
+        open_file_graph("%s", w=%i, h=%i, svg=svg)
+        """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+        txt+= """
+        par(mar=c(10,2,2,2))
+        gg <- ggplot(data=nptt, aes(x=Var1,y=Freq,fill=Var2)) + geom_area(alpha=1 , size=0.5, colour="black")
+        gg + scale_fill_manual(values=col)
+        dev.off()
+        """
+        self.add(txt)
+        self.write()
+
+class DendroScript(PrintRScript) :
+    def make_script(self) :
+        if self.parametres['svg'] :
+            typefile = '.svg'
+        else :
+            typefile = '.png'
+        fileout = self.parametres['fileout']
+        width = self.parametres['width']
+        height = self.parametres['height']
+        type_dendro = self.parametres['dendro_type']
+        if self.parametres['taille_classe'] :
+            tclasse = 'TRUE'
+        else :
+            tclasse = 'FALSE'
+        if self.parametres['color_nb'] == 0 :
+            bw = 'FALSE'
+        else :
+            bw = 'TRUE'
+        if self.parametres['type_tclasse'] == 0 :
+            histo='FALSE'
+        else :
+            histo = 'TRUE'
+        if self.parametres['svg'] :
+            svg = 'TRUE'
+        else :
+            svg = 'FALSE'
+        dendro_path = self.pathout['Rdendro']
+        classe_path = self.pathout['uce']
+        txt = """
+        library(ape)
+        load("%s")
+        source("%s")
+        classes <- read.csv2("%s", row.names=1)
+        classes <- classes[,1]
+        """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']),  ffr(classe_path))
+        if self.parametres['dendro'] == 'simple' :
+            txt += """
+            open_file_graph("%s", width=%i, height=%i, svg=%s)
+            plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s)
+            """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse)
+        elif self.parametres['dendro'] == 'texte' :
+            txt += """
+            load("%s")
+            source("%s")
+            if (is.null(debsup)) {
+                debsup <- debet
+            }
+            chistable <- chistabletot[1:(debsup-1),]
+            """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']))
+            if self.parametres.get('translation', False) :
+                txt += """
+                rn <- read.csv2("%s", header=FALSE, sep='\t')
+                rnchis <- row.names(chistable)
+                commun <- intersect(rnchis, unique(rn[,2]))
+                idrnchis <- sapply(commun, function(x) {which(rnchis==x)})
+                idrn <- sapply(commun, function(x) {which(as.vector(rn[,2])==x)[1]})
+                rownames(chistable)[idrnchis] <- as.vector(rn[idrn,1])
+                """ % ffr(self.parametres['translation'])
+            txt += """
+            open_file_graph("%s", width=%i, height=%i, svg = %s)
+            plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL)
+            """ % (ffr(fileout), width, height, svg, type_dendro, bw)
+        elif self.parametres['dendro'] == 'cloud' :
+            txt += """
+            load("%s")
+            source("%s")
+            if (is.null(debsup)) {
+                debsup <- debet
+            }
+            chistable <- chistabletot[1:(debsup-1),]
+            open_file_graph("%s", width=%i, height=%i, svg=%s)
+            plot.dendro.cloud(tree.cut1$tree.cl, classes, chistable, nbbycl = 300, type.dendro="%s", bw=%s, lab=NULL)
+            """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']), ffr(fileout), width, height, svg, type_dendro, bw)
+        self.add(txt)
+        self.write()
+
+
+class ReDoProfScript(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']])
+        print self.parametres
+