+class DendroScript(PrintRScript) :
+ def make_script(self) :
+ if self.parametres['svg'] :
+ typefile = '.svg'
+ else :
+ typefile = '.png'
+ fileout = self.parametres['fileout']
+ width = self.parametres['width']
+ height = self.parametres['height']
+ type_dendro = self.parametres['dendro_type']
+ if self.parametres['taille_classe'] :
+ tclasse = 'TRUE'
+ else :
+ tclasse = 'FALSE'
+ if self.parametres['color_nb'] == 0 :
+ bw = 'FALSE'
+ else :
+ bw = 'TRUE'
+ if self.parametres['type_tclasse'] == 0 :
+ histo='FALSE'
+ else :
+ histo = 'TRUE'
+ if self.parametres['svg'] :
+ svg = 'TRUE'
+ else :
+ svg = 'FALSE'
+ dendro_path = self.pathout['Rdendro']
+ classe_path = self.pathout['uce']
+ txt = """
+ library(ape)
+ load("%s")
+ source("%s")
+ classes <- read.csv2("%s", row.names=1)
+ classes <- classes[,1]
+ """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path))
+ if self.parametres['dendro'] == 'simple' :
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s)
+ """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse)
+ elif self.parametres['dendro'] == 'texte' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']))
+ if self.parametres.get('translation', False) :
+ txt += """
+ rn <- read.csv2("%s", header=FALSE, sep='\t')
+ rnchis <- row.names(chistable)
+ commun <- intersect(rnchis, unique(rn[,2]))
+ idrnchis <- sapply(commun, function(x) {which(rnchis==x)})
+ idrn <- sapply(commun, function(x) {which(as.vector(rn[,2])==x)[1]})
+ rownames(chistable)[idrnchis] <- as.vector(rn[idrn,1])
+ """ % ffr(self.parametres['translation'])
+ txt += """
+ open_file_graph("%s", width=%i, height=%i, svg = %s)
+ plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(fileout), width, height, svg, type_dendro, bw)
+ elif self.parametres['dendro'] == 'cloud' :
+ txt += """
+ load("%s")
+ source("%s")
+ if (is.null(debsup)) {
+ debsup <- debet
+ }
+ chistable <- chistabletot[1:(debsup-1),]
+ open_file_graph("%s", width=%i, height=%i, svg=%s)
+ plot.dendro.cloud(tree.cut1$tree.cl, classes, chistable, nbbycl = 300, type.dendro="%s", bw=%s, lab=NULL)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph']), ffr(fileout), width, height, svg, type_dendro, bw)
+ self.add(txt)
+ self.write()
+
+
+class ReDoProfScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']])
+ print self.parametres