+
+class ChronoggScript(PrintRScript):
+
+ def make_script(self):
+ self.sources([self.analyse.parent.RscriptsPath['Rgraph']])
+ print(self.parametres)
+ txt = """
+ library(ggplot2)
+ inRData <- "%s"
+ dendrof <- "%s"
+ load(inRData)
+ load(dendrof)
+ """ % (ffr(self.pathout['RData.RData']), ffr(self.pathout['dendrogramme.RData']))
+ txt += """
+ svg <- %s
+ """ % self.parametres['svg']
+ txt += """
+ tc <- which(grepl("%s",rownames(chistabletot)))
+ rn <- rownames(chistabletot)[tc]
+ tc <- tc[order(rn)]
+ dpt <- chistabletot[tc,]
+ tot <- afctable[tc,]
+ tcp <- rowSums(tot)
+ ptc <- tcp/sum(tcp)
+ dpt <- t(dpt)
+ dd <- dpt
+ """ % self.parametres['var'].replace('*', "\\\\*")
+ txt += """
+ classes <- n1[,ncol(n1)]
+ tcl <- table(classes)
+ if ('0' %in% names(tcl)) {
+ to.vire <- which(names(tcl) == '0')
+ tcl <- tcl[-to.vire]
+ }
+ tclp <- tcl/sum(tcl)
+ ptt <- prop.table(as.matrix(tot), 1)
+ ptt <- ptt[,as.numeric(tree.cut1$tree.cl$tip.label)]
+ rownames(ptt) <- cumsum(ptc)
+ nptt<-as.data.frame(as.table(ptt))
+ nptt[,1]<-as.numeric(as.character(nptt[,1]))
+ col <- rainbow(ncol(ptt))[as.numeric(tree.cut1$tree.cl$tip.label)]
+ """
+ txt += """
+ open_file_graph("%s", w=%i, h=%i, svg=svg)
+ """ % (ffr(self.parametres['tmpgraph']), self.parametres['width'], self.parametres['height'])
+ txt+= """
+ par(mar=c(10,2,2,2))
+ gg <- ggplot(data=nptt, aes(x=Var1,y=Freq,fill=Var2)) + geom_area(alpha=1 , size=0.5, colour="black")
+ gg + scale_fill_manual(values=col)
+ dev.off()
+ """
+ self.add(txt)
+ self.write()
+
+
+class DendroScript(PrintRScript):
+
+ def make_script(self):
+ if self.parametres['svg']: