+ self.write()
+
+class LabbeScript(PrintRScript) :
+ def make_script(self) :
+ self.sources([self.analyse.parent.RscriptsPath['distance-labbe.R'],
+ self.analyse.parent.RscriptsPath['Rgraph']])
+ txt = """
+ tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1)
+ """ % (self.pathout['tableafcm.csv'])
+ txt += """
+ dist.mat <- dist.labbe(tab)
+ dist.mat <- as.dist(dist.mat, upper=F, diag=F)
+ write.table(as.matrix(dist.mat), "%s", sep='\t')
+ library(cluster)
+ library(ape)
+ chd <- hclust(dist.mat, method="ward.D2")
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ par(cex=1.2)
+ plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
+ dev.off()
+ """ % (self.pathout['distmat.csv'], self.pathout['dist-labbe.png'])
+ self.add(txt)
+ self.write()
+
+