X-Git-Url: http://iramuteq.org/git?p=iramuteq;a=blobdiff_plain;f=PrintRScript.py;h=a4ed14dfb6d8948ca93df01083e92695ef1d860f;hp=25adb52ee69e9fc4e11b92991884820c1ad043cf;hb=238d461ff111b1bc3302494de4d9b630f9e9f623;hpb=b19770356272772c8c8ba75f351520eca186bd19

diff --git a/PrintRScript.py b/PrintRScript.py
index 25adb52..a4ed14d 100644
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 #Author: Pierre Ratinaud
 #Copyright (c) 2008-2011 Pierre Ratinaud
-#Lisense: GNU/GPL
+#License: GNU/GPL
 
 import tempfile
 from chemins import ffr
@@ -33,7 +33,7 @@ class PrintRScript :
 
     def sources(self, lsources) :
         for source in lsources :
-            self.add('source("%s")' % source)
+            self.add('source("%s", encoding = \'utf8\')' % source)
 
     def packages(self, lpks) :
         for pk in lpks :
@@ -211,7 +211,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
 #    open_file_graph("%s", widt = 600, height=400)
 #    plot(tree.tot1$tree.cl)
 #    dev.off()
-    """%DicoPath['arbre1']
+    """ % DicoPath['arbre1']
     
     if classif_mode == 0:
         txt += """
@@ -293,7 +293,7 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl)
     n1 <- chd.result$n1
     classeuce1 <- chd.result$cuce1
-    """ % (DicoPath['mat01'], DicoPath['listeuce1'], DicoPath['uce'])
+    """ % (DicoPath['mat01.csv'], DicoPath['listeuce1'], DicoPath['uce'])
     
     txt += """
     tree_tot1 <- make_tree_tot(chd.result$chd)
@@ -390,13 +390,15 @@ write.csv2(gbcluster,file="%s")
     xyminmax <- PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
     """ % (DictChdTxtOut['AFC2DL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2])
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
     """ % (DictChdTxtOut['AFC2DSL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2])
+        if ((fin - debet) > 2) {
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='coord', deb=debet, fin=fin, xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active = FALSE)
+        }
     """ % (DictChdTxtOut['AFC2DEL_OUT'])
         txt += """
-    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2])
+    PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE)
     """ % (DictChdTxtOut['AFC2DCL_OUT'])
 #        txt += """
  #   PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab)
@@ -533,16 +535,17 @@ 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
         txt = """
@@ -574,58 +577,68 @@ 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 + (20*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(2,2,1,0))
-        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))
-        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'):
@@ -708,8 +721,12 @@ 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 {
@@ -738,8 +755,12 @@ 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 {
@@ -837,11 +858,28 @@ class PrintSimiScript(PrintRScript) :
         if self.parametres['type_graph'] == 1 : 
             graphnb = 1
             type = 'nplot'
-            dirout = os.path.dirname(self.pathout['mat01'])
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
             while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')):
                 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 = 'web'
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
+            while os.path.exists(os.path.join(dirout,'web_'+str(graphnb))):
+                graphnb +=1
+            self.filename = ffr(os.path.join(dirout,'web_'+str(graphnb)))
+            os.mkdir(self.filename)        
+            self.filename = os.path.join(self.filename, 'gexf.gexf')
+        if self.parametres['type_graph'] == 4 : 
+            graphnb = 1
+            type = 'rglweb'
+            dirout = os.path.dirname(self.pathout['mat01.csv'])
+            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'
@@ -893,6 +931,9 @@ class PrintSimiScript(PrintRScript) :
             """
         txt += """
         seuil <- %s
+        if (method!='cooc') {
+            seuil <- seuil/100
+        } 
         """ % seuil
         
         txt += """
@@ -1015,7 +1056,7 @@ class PrintSimiScript(PrintRScript) :
                     """
             else :
                 txt+="""
-                label.cex <- NULL
+                label.cex <- cex
                 """
             if self.parametres.get('sfromchi', False) :
                 txt += """
@@ -1026,7 +1067,8 @@ 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]
@@ -1041,12 +1083,12 @@ 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
@@ -1090,7 +1132,14 @@ class WordCloudRScript(PrintRScript) :
         self.packages(['wordcloud'])
         bg_col = Rcolor(self.parametres['col_bg'])
         txt_col = Rcolor(self.parametres['col_text'])
+        if self.parametres['svg'] :
+            svg = 'TRUE'
+        else :
+            svg = 'FALSE'
         txt = """
+        svg <- %s
+        """ % svg
+        txt += """
         act <- read.csv2("%s", header = FALSE, row.names=1, sep='\t')
         selected.col <- read.table("%s")
         toprint <- as.matrix(act[selected.col[,1] + 1,])
@@ -1100,10 +1149,63 @@ class WordCloudRScript(PrintRScript) :
             toprint <- as.matrix(toprint[order(toprint[,1], decreasing=TRUE),])
             toprint <- as.matrix(toprint[1:maxword,])
         }
-        open_file_graph("%s", width = %i, height = %i)
+        open_file_graph("%s", width = %i, height = %i , svg = svg)
         par(bg=rgb%s)
         wordcloud(row.names(toprint), toprint[,1], scale=c(%f,%f), random.order=FALSE, colors=rgb%s)
         dev.off()
         """ % (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()
+
+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))
+        }
+        errort <- function(x) {
+            qt(0.975,df=lenght(x)-1)*sd(x)/sqrt(lenght(x))
+        }
+        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), type = '%s')
+        dev.off()
+        """ % (self.analyse.pathout['table.csv'], self.analyse.pathout['proto.png'], self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
+        self.add(txt)
+        self.write()
+
+
+class ExportAfc(PrintRScript) :
+    def make_script(self) :
+        self.source([self.analyse.parent.RscriptsPath['Rgraph']])
+        self.packages(['rgexf'])
+        txt = """
+        """
+
+class TgenSpecScript(PrintRScript):
+    def make_script(self):
+        self.packages(['textometry'])
+        txt = """
+        tgen <- read.csv2("%s", row.names = 1, sep = '\\t')
+        """ % ffr(self.parametres['tgeneff'])
+        txt += """
+        tot <- tgen[nrow(tgen), ]
+        result <- NULL
+        tgen <- tgen[-nrow(tgen),]
+        for (i in 1:nrow(tgen)) {
+            mat <- rbind(tgen[i,], tot - tgen[i,])
+            specmat <- specificities(mat)
+            result <- rbind(result, specmat[1,])
+        }
+        colnames(result) <- colnames(tgen)
+        row.names(result) <- rownames(tgen)
+        write.table(result, file = "%s", sep='\\t', col.names = NA)
+        """ % self.pathout['tgenspec.csv']
+        self.add(txt)
+