...

[iramuteq] / PrintRScript.py

diff --git a/PrintRScript.py b/PrintRScript.py
index 7f7e4c2..f9d7be3 100644 (file)
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -238,7 +238,7 @@ 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()
         """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2']))
         
@@ -704,7 +704,7 @@ 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"
@@ -740,7 +740,7 @@ 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"
@@ -1072,7 +1072,7 @@ 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]
@@ -1080,7 +1080,7 @@ 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])
                 """
@@ -1092,7 +1092,7 @@ 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
@@ -1210,6 +1210,31 @@ 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 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()  
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