X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=db2eeac22288e3e7a1c4e0a12cf0c9372293d2fa;hp=381733588f9888339b2085c93a08a9fda56ac1e1;hb=1fb687c23b19ae4cc88146acf393041356c1df3a;hpb=44b2ba75167b1ed5508e2f110130805bfe43a3bd

diff --git a/PrintRScript.py b/PrintRScript.py
index 3817335..db2eeac 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -148,8 +148,9 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False
         data2 <- as(data2, "dgCMatrix")
         row.names(data2) <- 1:nrow(data2)
         """ % DicoPath['TableUc2']
+    #log.info('ATTENTION ############# MODEPATATE ####################')
     txt += """
-    chd1<-CHD(data1, x = nbt, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
+    chd1<-CHD(data1, x = nbt, mode.patate = FALSE, libsvdc = libsvdc, libsvdc.path = libsvdc.path)
     """
     
     if classif_mode == 0:
@@ -172,12 +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)
@@ -206,7 +207,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, libsvdc = False
     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()
@@ -365,33 +366,41 @@ write.csv2(gbcluster,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 = '')
+        #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 = '')
         """
     
         txt += """
     PARCEX<-%s
+    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)
+    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)
     """ % (DictChdTxtOut['AFC2DL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab)
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
     """ % (DictChdTxtOut['AFC2DSL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab)
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
     """ % (DictChdTxtOut['AFC2DEL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab)
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin=xmin, xmax=xmax, ymin = ymin, ymax=ymax)
     """ % (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 += """
+ #   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)
@@ -417,12 +426,18 @@ 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()
 
@@ -438,6 +453,8 @@ 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'], \
@@ -450,7 +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):
@@ -460,10 +478,12 @@ 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")
@@ -523,9 +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)
@@ -541,7 +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)]
@@ -632,29 +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 += """
@@ -663,27 +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 : 
@@ -781,13 +846,13 @@ class PrintSimiScript(PrintRScript) :
             txt += """
             et <- list()
             """
-            for i,et in enumerate(self.tableau.etline) :
+            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)
@@ -812,7 +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' 
@@ -910,20 +975,26 @@ class PrintSimiScript(PrintRScript) :
         self.add(txt)
         self.write()
 
-WordCloudRScript(PrintRScript) :
+class WordCloudRScript(PrintRScript) :
     def make_script(self) :
-        self.Source([self.analyse.parent.RscriptsPath['Rgraph']])
+        self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
         self.packages(['wordcloud'])
         bg_col = Rcolor(self.parametres['col_bg'])
         txt_col = Rcolor(self.parametres['col_text'])
         txt = """
         act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
         selected.col <- read.table("%s")
-        toprint <- act[selected.col + 1,]
+        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)
         par(bg=rgb%s)
         wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
         dev.off()
-        """ % (self.parametres['actives_eff.csv'], self.parametres['selected.csv'], self.parametres['graphout'], self.parametres['width'], self.parametres['height'], bg_col, self.parametres['maxcex'], self.parametres['mincex'], txt_col)
+        """ % (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()