X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=deaddf51ced131c513700e1eda655a5e86b25a58;hp=4d0fb40fcaad3634a92fd3ad88a1869a9d0234e4;hb=3d1a621b481e251f8a086af586c7eb0bb87b0004;hpb=8fa853a25a9d62b1446e1bc543e5a3a4d0e03dcf

diff --git a/PrintRScript.py b/PrintRScript.py
index 4d0fb40..deaddf5 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #Author: Pierre Ratinaud
 #Copyright (c) 2008-2011 Pierre Ratinaud
-#Lisense: GNU/GPL
+#License: GNU/GPL
 
 import tempfile
 from chemins import ffr
@@ -17,8 +17,9 @@ class PrintRScript :
         log.info('Rscript')
         self.pathout = analyse.pathout
         self.analyse = analyse
+        self.parametres = analyse.parametres
         self.scriptout = self.pathout['temp']
-        self.script =  u"#Script genere par IRaMuTeQ - %s" % datetime.now().ctime()
+        self.script =  u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime()
     
     def add(self, txt) :
         self.script = '\n'.join([self.script, txt])
@@ -32,11 +33,15 @@ class PrintRScript :
 
     def sources(self, lsources) :
         for source in lsources :
-            self.add('source("%s")' % source)
+            self.add('source("%s", encoding = \'utf8\')' % ffr(source))
+
+    def packages(self, lpks) :
+        for pk in lpks :
+            self.add('library(%s)' % pk)
 
     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 :
@@ -46,6 +51,8 @@ class PrintRScript :
 class chdtxt(PrintRScript) :
     pass
 
+def Rcolor(color) :
+    return str(color).replace(')', ', max=255)')
 
 class Alceste2(PrintRScript) :
     def doscript(self) :
@@ -102,13 +109,13 @@ class Alceste2(PrintRScript) :
 #
 
 
-def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False, libsvdc_path = None, R_max_mem = False):
+def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False):
     txt = """
     source("%s")
     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)
@@ -117,93 +124,112 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False
     txt += """
     nbt <- %i
     """ % nbt
-    if libsvdc :
+    if svdmethod == 'svdlibc' and libsvdc :
         txt += """
-        libsvdc <- TRUE
+        svd.method <- 'svdlibc'
         libsvdc.path <- "%s"
         """ % ffr(libsvdc_path)
+    elif svdmethod == 'irlba' :
+        txt += """
+        library(irlba)
+        svd.method <- 'irlba'
+        libsvdc.path <- NULL
+        """
     else :
         txt += """
-        libsvdc <- FALSE
+        svd.method = 'svdR'
         libsvdc.path <- NULL
         """
-
+    if mode_patate :
+        txt += """
+        mode.patate = TRUE
+        """
+    else :
+        txt += """
+        mode.patate = FALSE
+        """
     txt +="""
     library(Matrix)
     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, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
+    chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)
     """
     
     if classif_mode == 0:
         txt += """
-    chd2<-CHD(data2, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
+    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)
+    rm(data1)
     """
     
     if classif_mode == 0:
         txt += """
-#        rm(data2)
+        rm(data2)
         """
     txt += """
-    chd.result <- Rchdtxt("%s",mincl=%i,classif_mode=%i, nbt = nbt)
+    classif_mode <- %i
+    mincl <- %i
+    uceout <- "%s"
+    if (classif_mode == 0) {
+        chd.result <- Rchdtxt(uceout, chd1, chd2 = chd2, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+    } else {
+        chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt)
+    }
     n1 <- chd.result$n1
     classeuce1 <- chd.result$cuce1
-    classeuce2 <- chd.result$cuce2
-    """ % (DicoPath['uce'], mincl, classif_mode)
+    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$tree.cl,classes)
+    plot.dendropr(tree.cut1$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 += """
@@ -212,21 +238,22 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False
         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()
 
 def RPamTxt(corpus, RscriptPath):
-    DicoPath = corpus.dictpathout
-    param = corpus.parametre
-    print param
+    DicoPath = corpus.pathout
+    param = corpus.parametres
     txt = """
     source("%s")
     """ % (RscriptPath['pamtxt'])
@@ -256,7 +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
@@ -267,14 +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['Act01'], 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)
@@ -282,27 +309,28 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     save(tree.cut1, file="%s")
     open_file_graph("%s", width = 600, height=400)
     classes<-n1[,ncol(n1)]
-    plot.dendropr(tree_cut1$tree.cl,classes)
-    """ % (DicoPath['Rdendro'],DicoPath['dendro1'])
+    plot.dendropr(tree_cut1$tree.cl,classes, histo = TRUE)
+    """ % (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)
@@ -310,7 +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=' ')
@@ -327,7 +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)
@@ -347,7 +375,7 @@ write.csv2(gbcluster,file="%s")
     #FIXME : split this!!!
         txt += """
     source("%s")
-    """ % RscriptsPath['Rgraph']
+    """ % ffr(RscriptsPath['Rgraph'])
     
         txt += """
         afc <- summary.ca.dm(afc)
@@ -355,36 +383,31 @@ write.csv2(gbcluster,file="%s")
         write.csv2(afc_table$facteur, file = "%s")
         write.csv2(afc_table$colonne, file = "%s")
         write.csv2(afc_table$ligne, file = "%s")
-        """ % (DictChdTxtOut['afc_facteur'], DictChdTxtOut['afc_col'], DictChdTxtOut['afc_row'])
-    
-        txt += """
-        xlab <- paste('facteur 1 - ', round(afc$facteur[1,2],2), sep = '')
-        ylab <- paste('facteur 2 - ', round(afc$facteur[2,2],2), sep = '')
-        xlab <- paste(xlab, ' %', sep = '')
-        ylab <- paste(ylab, ' %', sep = '')
-        """
+        """ % (ffr(DictChdTxtOut['afc_facteur']), ffr(DictChdTxtOut['afc_col']), ffr(DictChdTxtOut['afc_row']))
     
         txt += """
     PARCEX<-%s
     """ % taillecar
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DL_OUT'])
+    xyminmax <- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
+    """ % (ffr(DictChdTxtOut['AFC2DL_OUT']))
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DSL_OUT'])
+    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)
+    """ % (ffr(DictChdTxtOut['AFC2DSL_OUT']))
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DEL_OUT'])
-        txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DCL_OUT'])
+        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)
+        }
+    """ % (ffr(DictChdTxtOut['AFC2DEL_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)
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
-    """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
+    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)
+    """ % (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)
+  #  PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
+ #   PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab)
+ #   """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl'])
        
     txt += """
 #rm(dataact)
@@ -394,7 +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()
@@ -410,17 +433,23 @@ def write_afc_graph(self):
     if self.param['do_select_chi'] : do_select_chi = 'TRUE'
     else : do_select_chi = 'FALSE'
 
+    if self.param['do_select_chi_classe'] : do_select_chi_classe = 'TRUE'
+    else : do_select_chi_classe = 'FALSE'
+
     if self.param['cex_txt'] : cex_txt = 'TRUE'
     else : cex_txt = 'FALSE'
 
     if self.param['tchi'] : tchi = 'TRUE'
     else : tchi = 'FALSE'
 
+    if self.param['svg'] : svg = 'TRUE'
+    else : svg = 'FALSE'
+
     with open(self.RscriptsPath['afc_graph'], 'r') as f:
         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],\
@@ -431,6 +460,8 @@ def write_afc_graph(self):
     self.param['select_nb'],  \
     do_select_chi, \
     self.param['select_chi'], \
+    do_select_chi_classe, \
+    self.param['nbchic'], \
     cex_txt, \
     self.param['txt_min'], \
     self.param['txt_max'], \
@@ -443,7 +474,8 @@ def write_afc_graph(self):
     tchi,\
     self.param['tchi_min'],\
     self.param['tchi_max'],\
-    ffr(os.path.dirname(self.fileout)))
+    ffr(os.path.dirname(self.fileout)),\
+    svg)
     return scripts
         
 def print_simi3d(self):
@@ -453,10 +485,12 @@ def print_simi3d(self):
         movie = "'" + ffr(os.path.dirname(self.DictPathOut['RData'])) + "'"
     else :
         movie = 'NULL'
-    if self.section == 'chd_dist_quest' :
-        header = 'TRUE'
-    else :
-        header = 'FALSE'
+    
+    #if self.corpus.parametres['type'] == 'corpus' :
+    #    header = 'TRUE'
+    #else :
+    #    header = 'FALSE'
+    header = 'FALSE'
     txt += """
     dm<-read.csv2("%s",row.names=1,header = %s)
     load("%s")
@@ -503,66 +537,110 @@ def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False,
         """ % (ffr(dendro),ffr(rgraph),  ffr(tmpgraph))
     return txt
 
-def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
+def barplot(table, parametres, intxt = False) :
     if not intxt :
         txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')'
     #width = 100 + (15 * len(rownames)) + (100 * len(colnames))
     #height =  len(rownames) * 15
-    rownb = len(rownames)
+    rownb = len(parametres['rownames'])
     #if height < 400 :
     #    height = 400
-    rownames = 'c("' + '","'.join(rownames) + '")'
-    colnames = 'c("' + '","'.join(colnames) + '")'
+    rownames = 'c("' + '","'.join(parametres['rownames']) + '")'
+    colnames = 'c("' + '","'.join(parametres['colnames']) + '")'
+
     if not intxt :
         #FIXME
         txt = """
-            inf <- NA
             di <- matrix(data=%s, nrow=%i, byrow = TRUE)
-            di[is.na(di)] <- max(di, na.rm=TRUE) + 2
+            toinf <- which(di == Inf)
+            tominf <- which(di == -Inf)
+            if (length(toinf)) {
+                di[toinf] <- NA
+                valmax <- max(di, na.rm = TRUE)
+                if (valmax <= 0) {
+                    valmax <- 2
+                } else {
+                    valmax <- valmax + 2
+                }
+                di[toinf] <- valmax
+            }
+            if (length(tominf)) {
+                di[tominf] <- NA
+                valmin <- min(di, na.rm = TRUE)
+                if (valmin >=0) {
+                    valmin <- -2
+                } else {
+                    valmin <- valmin - 2
+                }
+                di[tominf] <- valmin
+            }
             rownames(di)<- %s
             colnames(di) <- %s
         """ % (txttable, rownb, rownames, colnames)
     else :
         txt = intxt
-    txt += """
-        source("%s")
-        color = rainbow(nrow(di))
-        width <- 100 + (20*length(rownames(di))) + (100 * length(colnames(di)))
-        height <- nrow(di) * 15
-        if (height < 400) { height <- 400}
-        open_file_graph("%s",width = width, height = height)
-    	par(mar=c(0,0,0,0))
-	    layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(7)))
-        par(mar=c(2,2,1,0))
-        coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6))
-        c <- colMeans(coord)
-        c1 <- c[-1]
-        c2 <- c[-length(c)]
-        cc <- cbind(c1,c2)
-        lcoord <- apply(cc, 1, mean)
-        abline(v=lcoord)
-        if (min(di) < 0) {
-            amp <- abs(max(di) - min(di))
-        } else {
-            amp <- max(di)
-        }
-        if (amp < 10) {
-            d <- 2
-        } else {
-            d <- signif(amp%%/%%10,1)
-        }
-        mn <- round(min(di))
-        mx <- round(max(di))
-        for (i in mn:mx) {
-            if ((i/d) == (i%%/%%d)) { 
-                abline(h=i,lty=3)
+    if not 'tree' in parametres :
+        txt += """
+            source("%s")
+            color = rainbow(nrow(di))
+            width <- %i
+            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)))
+            par(mar=c(8,4,1,0))
+            yp = ifelse(length(toinf), 0.2, 0)
+            ym = ifelse(length(tominf), 0.2, 0)
+            ymin <- ifelse(!length(which(di < 0)), 0, min(di) - ym)
+            coord <- barplot(as.matrix(di), beside = TRUE, col = color, space = c(0.1,0.6), ylim=c(ymin, max(di) + yp), las = 2)
+            if (length(toinf)) {
+                coordinf <- coord[toinf]
+                valinf <- di[toinf]
+                text(x=coordinf, y=valinf + 0.1, 'i')
             }
-        }
-        par(mar=c(0,0,0,0))
-        plot(0, axes = FALSE, pch = '')
-        legend(x = 'center' , rownames(di), fill = color)
-        dev.off()
-        """ % (rgraph, ffr(tmpgraph))    
+            if (length(tominf)) {
+                coordinf <- coord[toinf]
+                valinf <- di[toinf]
+                text(x=coordinf, y=valinf - 0.1, 'i')
+            }            
+            c <- colMeans(coord)
+            c1 <- c[-1]
+            c2 <- c[-length(c)]
+            cc <- cbind(c1,c2)
+            lcoord <- apply(cc, 1, mean)
+            abline(v=lcoord)
+            if (min(di) < 0) {
+                amp <- abs(max(di) - min(di))
+            } else {
+                amp <- max(di)
+            }
+            if (amp < 10) {
+                d <- 2
+            } else {
+                d <- signif(amp%%/%%10,1)
+            }
+            mn <- round(min(di))
+            mx <- round(max(di))
+            for (i in mn:mx) {
+                if ((i/d) == (i%%/%%d)) { 
+                    abline(h=i,lty=3)
+                }
+            }
+            par(mar=c(0,0,0,0))
+            plot(0, axes = FALSE, pch = '')
+            legend(x = 'center' , rownames(di), fill = color)
+            dev.off()
+            """ % (ffr(parametres['rgraph']), parametres['width'], parametres['height'], ffr(parametres['tmpgraph']), parametres['svg'])    
+    else :
+        txt += """
+        load("%s")
+        library(ape)
+        source("%s")
+        width = %i
+        height = %i
+        open_file_graph("%s", width=width, height=height, svg = %s)
+        plot.dendro.lex(tree.cut1$tree.cl, di)
+        """ % (ffr(parametres['tree']), ffr(parametres['rgraph']), parametres['width'], parametres['height'], ffr(parametres['tmpgraph']), parametres['svg'])
     return txt
 
 #def RAfcUci(DictAfcUciOut, nd=2, RscriptsPath='', PARCEX='0.8'):
@@ -620,3 +698,565 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
 #    f.write(txt)
 #    f.close()
 
+class PrintSimiScript(PrintRScript) :
+    def make_script(self) :
+        self.txtgraph = ''
+        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' or self.parametres['type'] == 'simiclustermatrix') :
+            txt += """
+            dm.path <- "%s"
+            cn.path <- "%s"
+            selected.col <- "%s"
+            """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['actives.csv']), ffr(self.pathout['selected.csv']))
+            if 'word' in self.parametres :
+                txt += """
+                word <- TRUE
+                index <- %i + 1
+                """ % self.parametres['word']
+            else :
+                txt += """
+                word <- FALSE
+                """
+            txt += """
+            dm <-readMM(dm.path)
+            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)
+                sel.col <- sel.col[,1] + 1
+            } else {
+                sel.col <- 1:ncol(dm)
+            }
+            if (!word) {
+                dm <- dm[, sel.col]
+            } else {
+                forme <- colnames(dm)[index]
+                if (!index %in% sel.col) {
+                    sel.col <- append(sel.col, index)
+                }
+                dm <- dm[, sel.col]
+                index <- which(colnames(dm) == forme)
+            }
+            """
+        elif not self.parametres['keep_coord'] and (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'):
+            txt += """
+            dm.path <- "%s"
+            selected.col <- "%s"
+            """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['selected.csv']))
+            if 'word' in self.parametres :
+                txt += """
+                word <- TRUE
+                index <- %i + 1
+                """ % self.parametres['word']
+            else :
+                txt += """
+                word <- FALSE
+                """
+            txt += """
+            dm <-read.csv2(dm.path)
+            dm <- as.matrix(dm)
+            if (file.exists(selected.col)) {
+                sel.col <- read.csv2(selected.col, header = FALSE)
+                sel.col <- sel.col[,1] + 1
+            } else {
+                sel.col <- 1:ncol(dm)
+            }
+            if (!word) {
+                dm <- dm[, sel.col]
+            } else {
+                forme <- colnames(dm)[index]
+                if (!index %in% sel.col) {
+                    sel.col <- append(sel.col, index)
+                }
+                dm <- dm[, sel.col]
+                index <- which(colnames(dm) == forme)
+            }
+            """
+        else :
+            txt += """
+            load("%s")
+            """ % ffr(self.pathout['RData.RData'])
+        
+        if self.parametres['coeff'] == 0 :
+            method = 'cooc'
+            if not self.parametres['keep_coord'] :
+                txt += """
+                method <- 'cooc'
+                mat <- make.a(dm)
+                """
+        else :
+            if not self.parametres['keep_coord'] :
+                txt += """
+                dm <- as.matrix(dm)
+                """
+        if self.parametres['coeff'] == 1 :
+            method = 'prcooc'
+            txt += """
+            method <- 'Russel'
+            mat <- simil(dm, method = 'Russel', diag = TRUE, upper = TRUE, by_rows = FALSE)
+            """
+        elif self.analyse.indices[self.parametres['coeff']] == 'binomial' :
+            method = 'binomial'
+            if not self.parametres['keep_coord'] :
+                txt += """
+                method <- 'binomial'
+                mat <- binom.sim(dm)
+                """
+        elif self.parametres['coeff'] != 0 :
+            method = self.analyse.indices[self.parametres['coeff']]
+            if not self.parametres['keep_coord'] :
+                txt += """
+                method <-"%s"
+                mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE)
+                """ % self.analyse.indices[self.parametres['coeff']]
+        if not self.parametres['keep_coord'] :
+            txt += """
+            mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
+            mat[is.na(mat)] <- 0
+            if (length(which(mat == Inf))) {
+                infp <- which(mat == Inf)
+                mat[infp] <- NA
+                maxmat <- max(mat, na.rm = TRUE)
+                if (maxmat > 0) {
+                maxmat <- maxmat + 1
+                } else {
+                    maxmat <- 0
+                }
+                mat[infp] <- maxmat
+            }
+            if (length(which(mat == -Inf))) {
+                infm <- which(mat == -Inf)
+                mat[infm] <- NA
+                minmat <- min(mat, na.rm = TRUE)
+                if (maxmat < 0) {
+                minmat <- minmat - 1
+                } else {
+                    minmat <- 0
+                }
+                mat[infm] <- minmat
+            }
+            """
+        if 'word' in self.parametres and not self.parametres['keep_coord'] :
+            txt += """
+            mat <- graph.word(mat, index)
+            cs <- colSums(mat)
+            if (length(cs)) 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 self.parametres['layout'] == 0 : layout = 'random'
+        if self.parametres['layout'] == 1 : layout = 'circle'
+        if self.parametres['layout'] == 2 : layout = 'frutch'
+        if self.parametres['layout'] == 3 : layout = 'kawa'
+        if self.parametres['layout'] == 4 : layout = 'graphopt'
+
+
+        self.filename=''
+        if self.parametres['type_graph'] == 0 : type = 'tkplot'
+        if self.parametres['type_graph'] == 1 : 
+            graphnb = 1
+            type = 'nplot'
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
+            while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
+                graphnb +=1
+            self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png'))
+        if self.parametres['type_graph'] == 2 : type = 'rgl'
+        if self.parametres['type_graph'] == 3 : 
+            graphnb = 1
+            type = 'web'
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
+            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)        
+            self.filename = os.path.join(self.filename, 'gexf.gexf')
+        if self.parametres['type_graph'] == 4 : 
+            graphnb = 1
+            type = 'rglweb'
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
+            while os.path.exists(os.path.join(dirout,'webrgl_'+str(graphnb))):
+                graphnb +=1
+            self.filename = ffr(os.path.join(dirout,'webrgl_'+str(graphnb)))
+            os.mkdir(self.filename)
+
+        if self.parametres['arbremax'] : 
+            arbremax = 'TRUE'
+            self.txtgraph += ' - arbre maximum'
+        else : arbremax = 'FALSE'
+        
+        if self.parametres['coeff_tv'] : 
+            coeff_tv = self.parametres['coeff_tv_nb']
+            tvminmax = 'c(NULL,NULL)'
+        elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False) :
+            coeff_tv = 'NULL'
+            tvminmax = 'c(%i, %i)' %(self.parametres['tvmin'], self.parametres['tvmax'])
+        if self.parametres['coeff_te'] : coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax'])
+        else : coeff_te = 'NULL'
+        
+        if self.parametres['vcex'] or self.parametres.get('cexfromchi', False) :
+            vcexminmax = 'c(%i/10,%i/10)' % (self.parametres['vcexmin'],self.parametres['vcexmax'])
+        else :
+            vcexminmax = 'c(NULL,NULL)'
+        if not self.parametres['label_v'] : label_v = 'FALSE'
+        else : label_v = 'TRUE'
+
+        if not self.parametres['label_e'] : label_e = 'FALSE'
+        else : label_e = 'TRUE'
+        
+        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)')
+
+        txt += """
+        minmaxeff <- %s
+        """ % tvminmax
+        txt += """
+        vcexminmax <- %s
+        """ % vcexminmax
+        txt += """
+        cex = %i/10
+        """ % self.parametres['cex']
+
+        if self.parametres['film'] : 
+            txt += """
+            film <- "%s"
+            """ % self.pathout['film']
+        else : 
+            txt += """
+            film <- NULL
+            """
+        txt += """
+        seuil <- %s
+        if (!is.null(seuil)) {
+            if (method!='cooc') {
+                seuil <- seuil/100
+            } 
+        }
+        """ % seuil
+        
+        txt += """
+        label.v <- %s
+        label.e <- %s
+        """ % (label_v, label_e)
+        txt += """
+        cols <- rgb%s
+        cola <- rgb%s
+        """ % (cols, cola)
+        txt += """
+        width <- %i
+        height <- %i
+        """ % (self.parametres['width'], self.parametres['height'])
+        if self.parametres['keep_coord'] :
+            txt += """
+            coords <- try(coords, TRUE)
+            if (!is.matrix(coords)) {
+                coords<-NULL
+            }
+            """
+        else :
+            txt += """
+            coords <- NULL
+            """
+        txt += """
+        alpha <- %i/100
+        """ % self.parametres['alpha']
+        txt += """
+        alpha <- %i/100
+        """ % self.parametres['alpha']
+#############################################
+        if  self.parametres.get('bystar',False) :
+            txt += """
+            et <- list()
+            """
+            for i, line in enumerate(self.parametres['listet']) :
+                txt+= """
+                et[[%i]] <- c(%s)
+                """ % (i+1, ','.join([`val + 1` for val in line]))
+            txt+= """
+            unetoile <- c('%s')
+            """ % ("','".join([val for val in self.parametres['selectedstars']]))
+            txt += """
+            fsum <- NULL
+            rs <- rowSums(dm)
+            for (i in 1:length(unetoile)) {
+                print(unetoile[i])
+                tosum <- et[[i]]
+                if (length(tosum) > 1) {
+                    fsum <- cbind(fsum, colSums(dm[tosum,]))
+                } else {
+                    fsum <- cbind(fsum, dm[tosum,])
+                }
+            }
+            source("%s")
+            lex <- AsLexico2(fsum, chip=TRUE)
+            dcol <- apply(lex[[4]],1,which.max)
+            toblack <- apply(lex[[4]],1,max)
+            gcol <- rainbow(length(unetoile))
+            #gcol[2] <- 'orange'
+            vertex.label.color <- gcol[dcol]
+            vertex.label.color[which(toblack <= 3.84)] <- 'black'
+            leg <- list(unetoile=unetoile, gcol=gcol)  
+            cols <- vertex.label.color
+            chivertex.size <- norm.vec(toblack, vcexminmax[1],  vcexminmax[2])
+            
+            """ % (ffr(self.analyse.parent.RscriptsPath['chdfunct']))
+        else :
+            txt += """
+            vertex.label.color <- 'black' 
+            chivertex.size <- 1
+            leg<-NULL
+            """
+#############################################        
+
+#        txt += """
+#        eff <- colSums(dm)
+#        g.ori <- graph.adjacency(mat, mode='lower', weighted = TRUE)
+#        w.ori <- E(g.ori)$weight
+#        if (max.tree) {
+#            if (method == 'cooc') {
+#                E(g.ori)$weight <- 1 / w.ori
+#            } else {
+#                E(g.ori)$weigth <- 1 - w.ori
+#            }
+#            g.max <- minimum.spanning.tree(g.ori)
+#            if (method == 'cooc') {
+#                E(g.max)$weight <- 1 / E(g.max)$weight
+#            } else {
+#                E(g.max)$weight <- 1 - E(g.max)$weight
+#            }
+#            g.toplot <- g.max
+#        } else {
+#            g.toplot <- g.ori
+#        }
+#        """
+        if self.parametres['com'] :
+            com = `self.parametres['communities']`
+        else :
+            com = 'NULL'
+        if self.parametres['halo'] :
+            halo = 'TRUE'
+        else :
+            halo = 'FALSE'
+        txt += """
+        communities <- %s
+        halo <- %s
+        """ % (com, halo)
+        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)
+        """ % (method, type, layout, arbremax, coeff_tv, coeff_te)
+            
+        if self.parametres.get('bystar',False) :
+            if self.parametres.get('cexfromchi', False) :
+                txt+="""
+                    label.cex<-chivertex.size
+                    """
+            else :
+                txt+="""
+                label.cex <- cex
+                """
+            if self.parametres.get('sfromchi', False) :
+                txt += """
+                vertex.size <- norm.vec(toblack, minmaxeff[1], minmaxeff[2])
+                """
+            else :
+                txt += """
+                vertex.size <- NULL
+                """
+        else :
+            #print 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]
+                """ % ffr(self.parametres['tmpchi'])
+                txt += """
+                    lchi <- lchi[sel.col]
+                    """
+            if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) :
+                txt += """ 
+                label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2])
+                """
+            else :
+                txt += """
+            if (is.null(vcexminmax[1])) {
+                label.cex <- cex
+            } else {
+                label.cex <- graph.simi$label.cex
+            }
+            """
+            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
+                """
+            else :
+                txt += """
+            if (is.null(minmaxeff[1])) {
+                vertex.size <- 0
+            } else {
+                vertex.size <- graph.simi$eff
+            }
+            """
+        #txt += """ vertex.size <- NULL """
+        if self.parametres['svg'] : svg = 'TRUE'
+        else : svg = 'FALSE'
+        txt += """
+        svg <- %s
+        """ % svg
+        txt += """
+        vertex.col <- cols
+        if (!is.null(graph.simi$com)) {
+            com <- graph.simi$com
+            colm <- rainbow(length(com))
+            if (vertex.size != 0 || graph.simi$halo) {
+                vertex.label.color <- 'black'
+                vertex.col <- colm[membership(com)]
+            } else {
+                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, edge.curved = edge.curved, svg = svg)
+        save.image(file="%s")
+        """ % (type, self.filename, ffr(self.pathout['RData']))
+        
+        self.add(txt)
+        self.write()
+
+class WordCloudRScript(PrintRScript) :
+    def make_script(self) :
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+        self.packages(['wordcloud'])
+        bg_col = Rcolor(self.parametres['col_bg'])
+        txt_col = Rcolor(self.parametres['col_text'])
+        if self.parametres['svg'] :
+            svg = 'TRUE'
+        else :
+            svg = 'FALSE'
+        txt = """
+        svg <- %s
+        """ % svg
+        txt += """
+        act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
+        selected.col <- read.table("%s")
+        toprint <- as.matrix(act[selected.col[,1] + 1,])
+        rownames(toprint) <- rownames(act)[selected.col[,1] + 1]
+        maxword <- %i
+        if (nrow(toprint) > maxword) {
+            toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
+            toprint <- as.matrix(toprint[1:maxword,])
+        }
+        open_file_graph("%s", width = %i, height = %i , svg = svg)
+        par(bg=rgb%s)
+        wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
+        dev.off()
+        """ % (ffr(self.analyse.pathout['actives_eff.csv']), ffr(self.analyse.pathout['selected.csv']), self.parametres['maxword'], ffr(self.parametres['graphout']), self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)
+        self.add(txt)
+        self.write()
+
+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))
+        }
+        errort <- function(x) {
+            qt(0.975,df=lenght(x)-1)*sd(x)/sqrt(lenght(x))
+        }
+        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')
+        dev.off()
+        """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
+        self.add(txt)
+        self.write()
+
+
+class ExportAfc(PrintRScript) :
+    def make_script(self) :
+        self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+        self.packages(['rgexf'])
+        txt = """
+        """
+
+class TgenSpecScript(PrintRScript):
+    def make_script(self):
+        self.packages(['textometry'])
+        txt = """
+        tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+        """ % ffr(self.parametres['tgeneff'])
+        txt += """
+        tot <- tgen[nrow(tgen), ]
+        result <- NULL
+        tgen <- tgen[-nrow(tgen),]
+        for (i in 1:nrow(tgen)) {
+            mat <- rbind(tgen[i,], tot - tgen[i,])
+            specmat <- specificities(mat)
+            result <- rbind(result, specmat[1,])
+        }
+        colnames(result) <- colnames(tgen)
+        row.names(result) <- rownames(tgen)
+        write.table(result, file = "%s", sep='\\t', col.names = NA)
+        """ % 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