par(cex=1.2)
plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
dev.off()
- """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['dist-labbe.png']))
+ """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png']))
+ txt +="""
+ open_file_graph("%s", width=1000, height=1000, svg=F)
+ heatmap(as.matrix(dist.mat), symm = T, distfun=function(x) as.dist(x))
+ dev.off()
+ """ % ffr(self.pathout['labbe-heatmap.png'])
+ txt += """
+ #http://stackoverflow.com/questions/3081066/what-techniques-exists-in-r-to-visualize-a-distance-matrix
+ dst <- data.matrix(dist.mat)
+ dim <- ncol(dst)
+ rn <- row.names(as.matrix(dist.mat))
+ open_file_graph("%s", width=1500, height=1000, svg=F)
+ par(mar=c(10,10,3,3))
+ image(1:dim, 1:dim, dst, axes = FALSE, xlab="", ylab="")
+ axis(1, 1:dim, rn, cex.axis = 0.9, las=3)
+ axis(2, 1:dim, rn, cex.axis = 0.9, las=1)
+ text(expand.grid(1:dim, 1:dim), sprintf("%%0.2f", dst), cex=0.6)
+ dev.off()
+ """ % ffr(self.pathout['labbe-matrix.png'])
self.add(txt)
self.write()
layout(mat.graphic, heights=heights.graphic, widths=c(0.15,0.85))
par(mar=c(0,0,0,0))
tree.toplot <- tree.cut1$tree.cl
+ num.label <- as.numeric(tree.cut1$tree.cl$tip.label)
+ col.tree <- rainbow(length(num.label))[num.label]
tree.toplot$tip.label <- paste('classe ', tree.toplot$tip.label)
- plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T)
+ plot.phylo(tree.toplot,label.offset=0.1, cex=1.1, no.margin=T, x.lim=20, tip.color = col.tree)
for (i in clod) {
print(i)
par(mar=c(0,0,0,0))