X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=120e4ff7d7e411449fd8f208ecc643c2ac873fd6;hp=fae8dcb8869eec9b451aa4527d01cf29f64d8ace;hb=9420002b21cada767db876f972f6083fc542ccd2;hpb=a38c33bb022324119c865d990e7ef1f087c24780

diff --git a/PrintRScript.py b/PrintRScript.py
index fae8dcb..120e4ff 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -169,10 +169,6 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         txt += """
     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
@@ -203,18 +199,21 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     }
     n1 <- chd.result$n1
     classeuce1 <- chd.result$cuce1
-    classeuce2 <- chd.result$cuce2
-    """ % (classif_mode, mincl, DicoPath['uce'])
+    classes<-n1[,ncol(n1)]
+    write.csv2(n1, file="%s")
+    rm(n1)
+    """ % (classif_mode, mincl, DicoPath['uce'], 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']
+    """ % 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)
@@ -224,7 +223,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     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, histo=TRUE)
     open_file_graph("%s", width = 600, height=400)
@@ -244,8 +243,10 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         """ % (DicoPath['dendro2'], DicoPath['arbre2'])
         
     txt += """
-    save.image(file="%s")
-    """ % DicoPath['RData']
+    
+    #save.image(file="%s")
+    """ % (DicoPath['RData'])
+    
     fileout = open(DicoPath['Rchdtxt'], 'w')
     fileout.write(txt)
     fileout.close()
@@ -322,8 +323,9 @@ def AlcesteTxtProf(DictChdTxtOut, RscriptsPath, clnb, taillecar):
     txt = "clnb<-%i\n" % clnb
     txt += """
 source("%s")
-load("%s")
-""" % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'])
+#load("%s")
+n1 <- read.csv2("%s")
+""" % (RscriptsPath['chdfunct'], DictChdTxtOut['RData'], 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')
@@ -535,16 +537,16 @@ 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
@@ -577,58 +579,68 @@ def barplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False) :
         """ % (txttable, rownb, rownames, colnames)
     else :
         txt = intxt
-    txt += """
-        source("%s")
-        color = rainbow(nrow(di))
-        width <- 100 + (10*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(6,2,1,0))
-        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')
-        }
-        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)
+    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'):
@@ -921,6 +933,11 @@ class PrintSimiScript(PrintRScript) :
             """
         txt += """
         seuil <- %s
+        if (!is.null(seuil)) {
+            if (method!='cooc') {
+                seuil <- seuil/100
+            } 
+        }
         """ % seuil
         
         txt += """
@@ -1148,6 +1165,10 @@ 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))
@@ -1157,9 +1178,9 @@ class ProtoScript(PrintRScript) :
         }
         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))
+        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.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
         self.add(txt)
         self.write()
 
@@ -1176,7 +1197,7 @@ class TgenSpecScript(PrintRScript):
         self.packages(['textometry'])
         txt = """
         tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
-        """ % self.parametres['tgeneff']
+        """ % ffr(self.parametres['tgeneff'])
         txt += """
         tot <- tgen[nrow(tgen), ]
         result <- NULL