Mercurial > repos > bgruening > chemfp

diff nxn_clustering.py @ 38:02e03ac072cf draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:19:01 -0400
parents 73b8c87779ae
children 28c487eb8399
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--- a/nxn_clustering.py	Fri Mar 23 03:26:12 2018 -0400
+++ b/nxn_clustering.py	Tue May 07 13:19:01 2019 -0400
@@ -69,12 +69,10 @@
     distances  = distance_matrix( arena, args.tanimoto_threshold )
 
     if args.similarity_matrix:
-        distances.tofile( args.similarity_matrix )
+        numpy.savetxt(args.similarity_matrix, distances)
 
     if args.cluster_image:
-        linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
+        linkage = hcluster.linkage(distances, method="single", metric="euclidean")
+        hcluster.dendrogram(linkage, labels=arena.ids, leaf_rotation=90.)
+        pylab.savefig(args.cluster_image, format=args.oformat)
 
-        hcluster.dendrogram(linkage, labels=arena.ids)
-
-        pylab.savefig( args.cluster_image, format=args.oformat )
-