From bfb6f93d0cf379a4d3190f3de2332f49b2f90a21 Mon Sep 17 00:00:00 2001 From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr> Date: Wed, 27 May 2020 08:29:44 +0200 Subject: [PATCH] 0.1 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f9d0fee..aa03a44 100644 --- a/README.md +++ b/README.md @@ -114,7 +114,7 @@ hierarchical tree data.nwk minimum spanning tree data.graphml ``` Of note, using option `-e 0.05` causes the removal of the fifth profile (8.19% missing entries). -The pairwise distance matrix is written into _data.d_ (available in _src/_), and options `-m` and `-h` yield the creation of the files _data.graphml_ and _data.nwk_. +The pairwise distance matrix is written into _data.d_ (available in _example/_), and options `-m` and `-h` yield the creation of the files _data.graphml_ and _data.nwk_. **MST-based clustering from distance data** @@ -187,7 +187,7 @@ This will output: n c k silhouette noise silhouette [low avg up] noise aWallace1 [low avg up] noise aWallace2 [low avg up] nAUC silhouette [low avg up] nAUC aWallace1 [low avg up] nAUC aWallace2 [low avg up] 413 0.016691213 3 0.829778 0.763112 0.838848 0.918818 0.444911 0.977796 1.000000 0.998107 0.999338 1.000000 0.825384 0.899548 0.938995 1.000000 1.000000 1.000000 0.828055 0.978866 1.000000 ``` -Details of the corresponding clustering (3 classes) is written into file _clust.txt_ (available in _src/_). +Details of the corresponding clustering (3 classes) is written into file _clust.txt_ (available in _example/_). A silhouette plot can be easily drawn using the output of the following command line on _clust.txt_: ```bash grep -F " s=" clust.txt | sed 's/ s=//' | sed 1d -- GitLab