X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=db2eeac22288e3e7a1c4e0a12cf0c9372293d2fa;hp=8d85e7100e267c5eb9b0e5898befd1c6ba7ad653;hb=1fb687c23b19ae4cc88146acf393041356c1df3a;hpb=ea75400310e91c45b6a705119b2e33afc0933e3e

diff --git a/PrintRScript.py b/PrintRScript.py
index 8d85e71..db2eeac 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -173,12 +173,12 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False
         """ % 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)
@@ -374,10 +374,14 @@ write.csv2(gbcluster,file="%s")
     
         txt += """
     PARCEX<-%s
-    xmin <- min(afc$rowcoord[,1]) + (0.1 * min(afc$rowcoord[,1]))
-    xmax <- max(afc$rowcoord[,1]) + (0.1 * max(afc$rowcoord[,1]))
-    ymin <- min(afc$rowcoord[,2]) + (0.1 * min(afc$rowcoord[,2]))
-    ymax <- max(afc$rowcoord[,2]) + (0.1 * max(afc$rowcoord[,2]))
+    xmin <- min(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,1], na.rm = TRUE))
+    xmax <- max(afc$rowcoord[,1], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,1], na.rm = TRUE))
+    ymin <- min(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * min(afc$rowcoord[,2], na.rm = TRUE))
+    ymax <- max(afc$rowcoord[,2], na.rm = TRUE) + (0.1 * max(afc$rowcoord[,2], na.rm = TRUE))
+    print(xmin)
+    print(xmax)
+    print(ymin)
+    print(ymax)
     """ % taillecar
         txt += """
     PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
@@ -431,6 +435,9 @@ def write_afc_graph(self):
     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()
 
@@ -460,7 +467,8 @@ 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):
@@ -535,9 +543,29 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
     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)
@@ -553,7 +581,20 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
     	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))
+        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))
+        if (length(toinf)) {
+            coordinf <- coord[toinf]
+            valinf <- di[toinf]
+            text(x=coordinf, y=valinf + 0.1, 'i')
+        }
+        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)]
@@ -644,29 +685,37 @@ class PrintSimiScript(PrintRScript) :
         self.txtgraph = ''
         self.packages(['igraph', 'proxy', 'Matrix'])
         self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']])
-        txt = """
-        dm.path <- "%s"
-        cn.path <- "%s"
-        selected.col <- "%s"
-        """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
-        txt += """
-        dm <-readMM(dm.path)
-        cn <- read.table(cn.path, sep=';', quote='"')
-        colnames(dm) <- cn[,1]
-        sel.col <- read.csv2(selected.col)
-        dm <- dm[, sel.col[,1] + 1]
-        """
-
-        if self.parametres['coeff'] == 0 :
-            method = 'cooc'
+        txt = ''
+        if not self.parametres['keep_coord'] :
+            txt += """
+            dm.path <- "%s"
+            cn.path <- "%s"
+            selected.col <- "%s"
+            """ % (self.pathout['mat01.csv'], self.pathout['actives.csv'], self.pathout['selected.csv'])
             txt += """
-            method <- 'cooc'
-            mat <- make.a(dm)
+            dm <-readMM(dm.path)
+            cn <- read.table(cn.path, sep=';', quote='"')
+            colnames(dm) <- cn[,1]
+            sel.col <- read.csv2(selected.col)
+            dm <- dm[, sel.col[,1] + 1]
             """
         else :
             txt += """
-            dm <- as.matrix(dm)
-            """
+            load("%s")
+            """ % 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 += """
@@ -675,27 +724,31 @@ class PrintSimiScript(PrintRScript) :
             """
         elif self.analyse.indices[self.parametres['coeff']] == 'binomial' :
             method = 'binomial'
-            txt += """
-            method <- 'binomial'
-            mat <- binom.sim(dm)
-            """
+            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 += """
-            method <-"%s"
-            mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE)
-            """ % self.analyse.indices[self.parametres['coeff']]
-        txt += """
-        mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
-        mat[is.na(mat)] <- 0
-        mat[is.infinite(mat)] <- 0
-        """
+            mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE))
+            mat[is.na(mat)] <- 0
+            mat[is.infinite(mat)] <- 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 : 
@@ -793,14 +846,13 @@ class PrintSimiScript(PrintRScript) :
             txt += """
             et <- list()
             """
-            print self.parametres
-            for i,et in enumerate(self.parametres['stars']) :
+            for i, line in enumerate(self.parametres['listet']) :
                 txt+= """
                 et[[%i]] <- c(%s)
-                """ % (i+1, ','.join(et[1:]))
+                """ % (i+1, ','.join([`val + 1` for val in line]))
             txt+= """
             unetoile <- c('%s')
-            """ % ("','".join([val[0] for val in self.tableau.etline]))
+            """ % ("','".join([val for val in self.parametres['selectedstars']]))
             txt += """
             fsum <- NULL
             rs <- rowSums(dm)
@@ -825,7 +877,7 @@ class PrintSimiScript(PrintRScript) :
             cols <- vertex.label.color
             chivertex.size <- norm.vec(toblack, vcexminmax[1],  vcexminmax[2])
             
-            """ % (self.parent.RscriptsPath['chdfunct'])
+            """ % (self.analyse.parent.RscriptsPath['chdfunct'])
         else :
             txt += """
             vertex.label.color <- 'black'