From ed41d5312b4b7639be8565ecc50ef5820e398acf Mon Sep 17 00:00:00 2001
From: pierre <ratinaud@univ-tlse2.fr>
Date: Sun, 29 Sep 2024 18:33:31 +0200
Subject: [PATCH] List of distances
---
PrintRScript.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/PrintRScript.py b/PrintRScript.py
index 0ce0bfc..26e4900 100755
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -1397,7 +1397,8 @@ class LabbeScript(PrintRScript):
#rownames(dist.mat) <- colnames(tab)
dist.mat <- dist.labbe(tab)
dist.mat <- as.dist(dist.mat, upper=F, diag=F)
- write.table(as.matrix(dist.mat), "%s", sep='\t')
+ dist2list(dist.mat, "%s")
+ write.csv2(as.matrix(dist.mat), "%s")
library(cluster)
library(ape)
chd <- hclust(dist.mat, method="ward.D2")
@@ -1405,7 +1406,7 @@ class LabbeScript(PrintRScript):
par(cex=1.2)
plot.phylo(as.phylo(chd), type='unrooted', lab4ut="axial")
dev.off()
- """ % (ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png']))
+ """ % (ffr(self.pathout['listdist.csv']), ffr(self.pathout['distmat.csv']), ffr(self.pathout['labbe-tree.png']))
txt +="""
open_file_graph("%s", width=1000, height=1000, svg=F)
par(mar=c(10,1,1,10))
--
2.7.4