X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=fbcf5cf4f19a33df557c27de79441405494fc117;hp=757bd1e558a04e70a711a28824c6408906cc6c0a;hb=5249c446f605b92824c1b12fe390563450d90f3f;hpb=a6c0faa62f33e5e64ad7eab5b9d804be99c6759a

diff --git a/PrintRScript.py b/PrintRScript.py
index 757bd1e..fbcf5cf 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -33,7 +33,7 @@ class PrintRScript :
 
     def sources(self, lsources) :
         for source in lsources :
-            self.add('source("%s", encoding = \'utf8\')' % source)
+            self.add('source("%s", encoding = \'utf8\')' % ffr(source))
 
     def packages(self, lpks) :
         for pk in lpks :
@@ -41,7 +41,7 @@ class PrintRScript :
 
     def load(self, l) :
         for val in l :
-            self.add('load("%s")' % val)
+            self.add('load("%s")' % ffr(val))
 
     def write(self) :
         with open(self.scriptout, 'w') as f :
@@ -115,7 +115,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     source("%s")
     source("%s")
     source("%s")
-    """ % (RscriptPath['CHD'], RscriptPath['chdtxt'], RscriptPath['anacor'], RscriptPath['Rgraph'])
+    """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdtxt']), ffr(RscriptPath['anacor']), ffr(RscriptPath['Rgraph']))
     if R_max_mem :
         txt += """
     memory.limit(%i)
@@ -153,14 +153,14 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     data1 <- readMM("%s")
     data1 <- as(data1, "dgCMatrix")
     row.names(data1) <- 1:nrow(data1)
-    """ % DicoPath['TableUc1']
+    """ % ffr(DicoPath['TableUc1'])
     
     if classif_mode == 0:
         txt += """
         data2 <- readMM("%s")
         data2 <- as(data2, "dgCMatrix")
         row.names(data2) <- 1:nrow(data2)
-        """ % DicoPath['TableUc2']
+        """ % ffr(DicoPath['TableUc2'])
     txt += """
     chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)
     """
@@ -169,20 +169,16 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         txt += """
     chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)
     """
-    else:
-        txt += """
-    chd2<-chd1
-    """    
     
     txt += """
     #lecture des uce
     listuce1<-read.csv2("%s")
-    """ % DicoPath['listeuce1']
+    """ % ffr(DicoPath['listeuce1'])
     
     if classif_mode == 0:
         txt += """
         listuce2<-read.csv2("%s")
-        """ % DicoPath['listeuce2']
+        """ % ffr(DicoPath['listeuce2'])
         
     txt += """
     rm(data1)
@@ -203,34 +199,37 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     }
     n1 <- chd.result$n1
     classeuce1 <- chd.result$cuce1
-    classeuce2 <- chd.result$cuce2
-    """ % (classif_mode, mincl, DicoPath['uce'])
+    classes<-n1[,ncol(n1)]
+    write.csv2(n1, file="%s")
+    rm(n1)
+    """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1.csv']))
     
     txt += """
     tree.tot1 <- make_tree_tot(chd1)
 #    open_file_graph("%s", widt = 600, height=400)
 #    plot(tree.tot1$tree.cl)
 #    dev.off()
-    """%DicoPath['arbre1']
+    """ % ffr(DicoPath['arbre1'])
     
     if classif_mode == 0:
         txt += """
+        classeuce2 <- chd.result$cuce2
         tree.tot2 <- make_tree_tot(chd2)
 #        open_file_graph("%s", width = 600, height=400)
 #        plot(tree.tot2$tree.cl)
 #        dev.off()
-        """ % 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")
-    classes<-n1[,ncol(n1)]
+    
     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()
-    """ % (DicoPath['Rdendro'], DicoPath['dendro1'], DicoPath['arbre1'])
+    """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']), ffr(DicoPath['arbre1']))
     
     if classif_mode == 0:
         txt += """
@@ -239,13 +238,15 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         plot(tree.cut2$tree.cl)
         dev.off()
         open_file_graph("%s", width = 600, height=400)
-        plot(tree.cut1$dendro_tot_cl)
+        plot(tree.cut2$dendro_tot_cl)
         dev.off()
-        """ % (DicoPath['dendro2'], DicoPath['arbre2'])
+        """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
         
     txt += """
-    save.image(file="%s")
-    """ % DicoPath['RData']
+    
+    #save.image(file="%s")
+    """ % (ffr(DicoPath['RData']))
+    
     fileout = open(DicoPath['Rchdtxt'], 'w')
     fileout.write(txt)
     fileout.close()
@@ -282,7 +283,7 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     source("%s")
     source("%s")
     source("%s")
-    """ % (RscriptPath['CHD'], RscriptPath['chdquest'], RscriptPath['anacor'],RscriptPath['Rgraph'])
+    """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdquest']), ffr(RscriptPath['anacor']),ffr(RscriptPath['Rgraph']))
 
     txt += """
     nbt <- %i - 1
@@ -293,14 +294,14 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
     n1 <- chd.result$n1
     classeuce1 <- chd.result$cuce1
-    """ % (DicoPath['mat01.csv'], DicoPath['listeuce1'], DicoPath['uce'])
+    """ % (ffr(DicoPath['mat01.csv']), ffr(DicoPath['listeuce1']), ffr(DicoPath['uce']))
     
     txt += """
     tree_tot1 <- make_tree_tot(chd.result$chd)
     open_file_graph("%s", width = 600, height=400)
     plot(tree_tot1$tree.cl)
     dev.off()
-    """%DicoPath['arbre1']
+    """ % ffr(DicoPath['arbre1'])
     
     txt += """
     tree_cut1 <- make_dendro_cut_tuple(tree_tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt)
@@ -309,26 +310,27 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     open_file_graph("%s", width = 600, height=400)
     classes<-n1[,ncol(n1)]
     plot.dendropr(tree_cut1$tree.cl,classes, histo = TRUE)
-    """ % (DicoPath['Rdendro'],DicoPath['dendro1'])
+    """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']))
     
     txt += """
     save.image(file="%s")
-    """ % DicoPath['RData']
+    """ % ffr(DicoPath['RData'])
     fileout = open(DicoPath['Rchdquest'], 'w')
     fileout.write(txt)
     fileout.close()
     
-def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
+def ReinertTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
     txt = "clnb<-%i\n" % clnb
     txt += """
 source("%s")
-load("%s")
-""" % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
+#load("%s")
+n1 <- read.csv2("%s")
+""" % (ffr(RscriptsPath['chdfunct']), ffr(DictChdTxtOut['RData']), ffr(DictChdTxtOut['n1.csv']))
     txt += """
 dataact<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
 datasup<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
 dataet<-read.csv2("%s", header = FALSE, sep = ';',quote = '\"', row.names = 1, na.strings = 'NA')
-""" % (DictChdTxtOut['Contout'], DictChdTxtOut['ContSupOut'], DictChdTxtOut['ContEtOut'])
+""" % (ffr(DictChdTxtOut['Contout']), ffr(DictChdTxtOut['ContSupOut']), ffr(DictChdTxtOut['ContEtOut']))
     txt += """
 tablesqrpact<-BuildProf(as.matrix(dataact),n1,clnb)
 tablesqrpsup<-BuildProf(as.matrix(datasup),n1,clnb)
@@ -336,7 +338,7 @@ tablesqrpet<-BuildProf(as.matrix(dataet),n1,clnb)
 """
     txt += """
 PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5])
-""" % (DictChdTxtOut['PROFILE_OUT'], DictChdTxtOut['ANTIPRO_OUT'])
+""" % (ffr(DictChdTxtOut['PROFILE_OUT']), ffr(DictChdTxtOut['ANTIPRO_OUT']))
     txt += """
 colnames(tablesqrpact[[2]])<-paste('classe',1:clnb,sep=' ')
 colnames(tablesqrpact[[1]])<-paste('classe',1:clnb,sep=' ')
@@ -353,7 +355,7 @@ write.csv2(chistabletot,file="%s")
 write.csv2(ptabletot,file="%s")
 gbcluster<-n1
 write.csv2(gbcluster,file="%s")
-""" % (DictChdTxtOut['chisqtable'], DictChdTxtOut['ptable'], DictChdTxtOut['SbyClasseOut'])
+""" % (ffr(DictChdTxtOut['chisqtable']), ffr(DictChdTxtOut['ptable']), ffr(DictChdTxtOut['SbyClasseOut']))
     if clnb > 2 :
         txt += """
     library(ca)
@@ -373,7 +375,7 @@ write.csv2(gbcluster,file="%s")
     #FIXME : split this!!!
         txt += """
     source("%s")
-    """ % RscriptsPath['Rgraph']
+    """ % ffr(RscriptsPath['Rgraph'])
     
         txt += """
         afc <- summary.ca.dm(afc)
@@ -381,25 +383,25 @@ write.csv2(gbcluster,file="%s")
         write.csv2(afc_table$facteur, file = "%s")
         write.csv2(afc_table$colonne, file = "%s")
         write.csv2(afc_table$ligne, file = "%s")
-        """ % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
+        """ % (ffr(DictChdTxtOut['afc_facteur']), ffr(DictChdTxtOut['afc_col']), ffr(DictChdTxtOut['afc_row']))
     
         txt += """
     PARCEX<-%s
     """ % taillecar
         txt += """
     xyminmax <- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DL_OUT'])
+    """ % (ffr(DictChdTxtOut['AFC2DL_OUT']))
         txt += """
     PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
-    """ % (DictChdTxtOut['AFC2DSL_OUT'])
+    """ % (ffr(DictChdTxtOut['AFC2DSL_OUT']))
         txt += """
         if ((fin - debet) > 2) {
     PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active = FALSE)
         }
-    """ % (DictChdTxtOut['AFC2DEL_OUT'])
+    """ % (ffr(DictChdTxtOut['AFC2DEL_OUT']))
         txt += """
     PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
-    """ % (DictChdTxtOut['AFC2DCL_OUT'])
+    """ % (ffr(DictChdTxtOut['AFC2DCL_OUT']))
 #        txt += """
  #   PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
  #   PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
@@ -415,7 +417,7 @@ rm(tablesqrpact)
 rm(tablesqrpsup)
 rm(tablesqrpet)
 save.image(file="%s")
-""" % DictChdTxtOut['RData']
+""" % ffr(DictChdTxtOut['RData'])
     file = open(DictChdTxtOut['RTxtProfGraph'], 'w')
     file.write(txt)
     file.close()
@@ -447,7 +449,7 @@ def write_afc_graph(self):
         txt = f.read()
 
 #    self.DictPathOut['RData'], \
-    scripts = txt % (self.RscriptsPath['Rgraph'],\
+    scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\
     self.param['typegraph'], \
     self.param['what'], \
     self.param['facteur'][0],\
@@ -702,12 +704,12 @@ class PrintSimiScript(PrintRScript) :
         self.packages(['igraph', 'proxy', 'Matrix'])
         self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
         txt = ''
-        if not self.parametres['keep_coord'] and not self.parametres['type'] == 'simimatrix':
+        if not self.parametres['keep_coord'] and not (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix') :
             txt += """
             dm.path <- "%s"
             cn.path <- "%s"
             selected.col <- "%s"
-            """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
+            """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['actives.csv']), ffr(self.pathout['selected.csv']))
             if 'word' in self.parametres :
                 txt += """
                 word <- TRUE
@@ -738,11 +740,11 @@ class PrintSimiScript(PrintRScript) :
                 index <- which(colnames(dm) == forme)
             }
             """
-        elif not self.parametres['keep_coord'] and self.parametres['type'] == 'simimatrix' :
+        elif not self.parametres['keep_coord'] and (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'):
             txt += """
             dm.path <- "%s"
             selected.col <- "%s"
-            """ % (self.pathout['mat01.csv'], self.pathout['selected.csv'])
+            """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['selected.csv']))
             if 'word' in self.parametres :
                 txt += """
                 word <- TRUE
@@ -775,7 +777,7 @@ class PrintSimiScript(PrintRScript) :
         else :
             txt += """
             load("%s")
-            """ % self.pathout['RData.RData']
+            """ % ffr(self.pathout['RData.RData'])
         
         if self.parametres['coeff'] == 0 :
             method = 'cooc'
@@ -907,7 +909,16 @@ class PrintSimiScript(PrintRScript) :
         
         if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil'])
         else : seuil = 'NULL'
-            
+        
+        if not self.parametres.get('edgecurved', False) :
+            ec = 'FALSE'
+        else :
+            ec = 'TRUE'
+        
+        txt += """
+        edge.curved <- %s
+        """ % ec
+        
         cols = str(self.parametres['cols']).replace(')',', max=255)')
         cola = str(self.parametres['cola']).replace(')',',max=255)')
 
@@ -931,9 +942,11 @@ class PrintSimiScript(PrintRScript) :
             """
         txt += """
         seuil <- %s
-        if (method!='cooc') {
-            seuil <- seuil/100
-        } 
+        if (!is.null(seuil)) {
+            if (method!='cooc') {
+                seuil <- seuil/100
+            } 
+        }
         """ % seuil
         
         txt += """
@@ -1001,7 +1014,7 @@ class PrintSimiScript(PrintRScript) :
             cols <- vertex.label.color
             chivertex.size <- norm.vec(toblack, vcexminmax[1],  vcexminmax[2])
             
-            """ % (self.analyse.parent.RscriptsPath['chdfunct'])
+            """ % (ffr(self.analyse.parent.RscriptsPath['chdfunct']))
         else :
             txt += """
             vertex.label.color <- 'black' 
@@ -1068,7 +1081,7 @@ class PrintSimiScript(PrintRScript) :
                 """
         else :
             #print self.parametres
-            if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] == 'simimatrix' and 'tmpchi' in self.parametres): 
+            if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] in ['simimatrix','simiclustermatrix'] and 'tmpchi' in self.parametres): 
                 txt += """
                 lchi <- read.table("%s")
                 lchi <- lchi[,1]
@@ -1076,7 +1089,7 @@ class PrintSimiScript(PrintRScript) :
                 txt += """
                     lchi <- lchi[sel.col]
                     """
-            if self.parametres['type'] == 'clustersimitxt' and self.parametres.get('cexfromchi', False) :
+            if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) :
                 txt += """ 
                 label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
                 """
@@ -1088,7 +1101,7 @@ class PrintSimiScript(PrintRScript) :
                 label.cex <- graph.simi$label.cex
             }
             """
-            if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False):
+            if (self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix']) and self.parametres.get('sfromchi', False):
                 txt += """ 
                 vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
                 if (!length(vertex.size)) vertex.size <- 0
@@ -1119,9 +1132,9 @@ class PrintSimiScript(PrintRScript) :
                 vertex.label.color <- colm[membership(com)]
             }
         }
-        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, svg = svg)
+        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, self.pathout['RData'])
+        """ % (type, self.filename, ffr(self.pathout['RData']))
         
         self.add(txt)
         self.write()
@@ -1161,6 +1174,10 @@ class ProtoScript(PrintRScript) :
     def make_script(self) :
         self.sources([self.analyse.parent.RscriptsPath['Rgraph'], self.analyse.parent.RscriptsPath['prototypical.R']])
         self.packages(['wordcloud'])
+        if self.parametres.get('cloud', False) :
+            cloud = 'TRUE'
+        else :
+            cloud = 'FALSE'
         txt = """
         errorn <- function(x) {
             qnorm(0.975)*sd(x)/sqrt(lenght(n))
@@ -1170,9 +1187,9 @@ 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))
+        prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s')
         dev.off()
-        """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'])
+        """ % (ffr(self.analyse.pathout['table.csv']), ffr(self.analyse.pathout['proto.png']), self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
         self.add(txt)
         self.write()
 
@@ -1189,7 +1206,7 @@ class TgenSpecScript(PrintRScript):
         self.packages(['textometry'])
         txt = """
         tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
-        """ % self.parametres['tgeneff']
+        """ % ffr(self.parametres['tgeneff'])
         txt += """
         tot <- tgen[nrow(tgen), ]
         result <- NULL
@@ -1202,6 +1219,44 @@ class TgenSpecScript(PrintRScript):
         colnames(result) <- colnames(tgen)
         row.names(result) <- rownames(tgen)
         write.table(result, file = "%s", sep='\\t', col.names = NA)
-        """ % self.pathout['tgenspec.csv']
+        """ % ffr(self.pathout['tgenspec.csv'])
+        self.add(txt)
+        
+class TgenProfScript(PrintRScript):
+    def make_script(self):
+        self.sources([self.analyse.ira.RscriptsPath['chdfunct']])
+        txt = """
+        tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+        """ % ffr(self.parametres['tgeneff'])
+        txt += """
+        res <- build.prof.tgen(tgen)
+        write.table(res$chi2, file = "%s", sep='\\t', col.names = NA)
+        write.table(res$pchi2, file = "%s", sep='\\t', col.names = NA)
+        """ % (ffr(self.pathout['tgenchi2.csv']), ffr(self.pathout['tgenpchi2.csv']))
         self.add(txt)
         
+class FreqMultiScript(PrintRScript):
+    def make_script(self):
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+        txt = """
+        freq <- read.csv2("%s", row.names=1, sep='\\t', dec='.')
+        """ % ffr(self.pathout['frequences.csv'])
+        txt += """
+        toplot <- freq[order(freq[,2]) ,2]
+        toplot.names = rownames(freq)[order(freq[,2])]
+        h <- 80 + (20 * nrow(freq))
+        open_file_graph("%s",height=h, width=500)
+        par(mar=c(3,20,3,3))
+        barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq)))
+        dev.off()
+        """ % ffr(self.pathout['barplotfreq.png'])
+        txt += """
+        toplot <- freq[order(freq[,4]) ,4]
+        toplot.names = rownames(freq)[order(freq[,4])]
+        open_file_graph("%s",height=h, width=500)
+        par(mar=c(3,20,3,3))
+        barplot(toplot, names = toplot.names, horiz=TRUE, las =1, col = rainbow(nrow(freq)))
+        dev.off()
+        """ % ffr(self.pathout['barplotrow.png'])
+        self.add(txt)
+        self.write()  
\ No newline at end of file