From ff602f724b8fc80f4fa067dbbc830343c0b4bed4 Mon Sep 17 00:00:00 2001
From: Pierre <ratinaud@univ-tlse2.fr>
Date: Wed, 5 Jun 2013 23:16:52 +0200
Subject: [PATCH] ...

---
 PrintRScript.py | 43 ++++++++++++++++++++++++++++++++++---------
 ProfList.py     |  7 ++++++-
 2 files changed, 40 insertions(+), 10 deletions(-)

diff --git a/PrintRScript.py b/PrintRScript.py
index 636fe9e..d81d070 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -711,8 +711,12 @@ class PrintSimiScript(PrintRScript) :
             dm <-readMM(dm.path)
             cn <- read.table(cn.path, sep='\t', quote='"')
             colnames(dm) <- cn[,1]
-            sel.col <- read.csv2(selected.col, header = FALSE)
-            sel.col <- sel.col[,1] + 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 {
@@ -741,8 +745,12 @@ class PrintSimiScript(PrintRScript) :
             txt += """
             dm <-read.csv2(dm.path)
             dm <- as.matrix(dm)
-            sel.col <- read.csv2(selected.col, header = FALSE)
-            sel.col <- sel.col[,1] + 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 {
@@ -845,6 +853,14 @@ class PrintSimiScript(PrintRScript) :
                 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 = 'rglweb'
+            dirout = os.path.dirname(self.pathout['mat01'])
+            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'
@@ -1018,7 +1034,7 @@ class PrintSimiScript(PrintRScript) :
                     """
             else :
                 txt+="""
-                label.cex <- NULL
+                label.cex <- cex
                 """
             if self.parametres.get('sfromchi', False) :
                 txt += """
@@ -1029,7 +1045,8 @@ class PrintSimiScript(PrintRScript) :
                 vertex.size <- NULL
                 """
         else :
-            if self.parametres['type'] == 'clustersimitxt' : 
+            print self.parametres
+            if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] == 'simimatrix' and 'tmpchi' in self.parametres): 
                 txt += """
                 lchi <- read.table("%s")
                 lchi <- lchi[,1]
@@ -1044,12 +1061,12 @@ class PrintSimiScript(PrintRScript) :
             else :
                 txt += """
             if (is.null(vcexminmax[1])) {
-                label.cex <- NULL
+                label.cex <- cex
             } else {
                 label.cex <- graph.simi$label.cex
             }
             """
-            if self.parametres['type'] == 'clustersimitxt' and self.parametres.get('sfromchi', False) :
+            if (self.parametres['type'] == 'clustersimitxt' or self.parametres['type'] == 'simimatrix') and self.parametres.get('sfromchi', False):
                 txt += """ 
                 vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2])
                 if (!length(vertex.size)) vertex.size <- 0
@@ -1124,10 +1141,18 @@ class ProtoScript(PrintRScript) :
         self.packages(['wordcloud'])
         txt = """
         mat <- read.csv2("%s", header = FALSE, row.names=1, sep='\t', quote='"', dec='.')
-        open_file_graph("%s",height=600, width=600)
+        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))
         dev.off()
         """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'])
         self.add(txt)
         self.write()
 
+
+class ExportAfc(PrintRScript) :
+    def make_script(self) :
+        self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+        self.packages(['rgexf'])
+        txt = """
+        """
+         
diff --git a/ProfList.py b/ProfList.py
index 6c206ad..b64d633 100644
--- a/ProfList.py
+++ b/ProfList.py
@@ -431,6 +431,10 @@ class ProfListctrlPanel(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin, listmix.Col
 
     def quest_simi(self, evt) :
         tableau = self.Source.tableau
+        if self.tmpchi is None :
+            self.tmpchi = tempfile.mktemp(dir=self.Source.parent.TEMPDIR)
+            with open(self.tmpchi, 'w') as f:
+                f.write('\n'.join([str(val) for val in self.lchi]))
         tab = tableau.make_table_from_classe(self.cl, self.la)
         pathout = ConstructPathOut(self.Source.pathout.dirout, 'simi_classe_%i' %self.cl)
         self.filename = os.path.join(pathout,'mat01.csv')
@@ -468,7 +472,8 @@ class ProfListctrlPanel(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin, listmix.Col
                           'film': False,
                           'com' : 0,
                           'communities' : 0,
-                          'halo' : 0
+                          'halo' : 0,
+                          'tmpchi': self.tmpchi
                           }
         act = {}
         tableau.chi = {}
-- 
2.7.4