MorphoCluster Library / CLI

MorphoCluster comes with a library (and command line client) for feature extraction, clustering and to work with MorphoCluster tree files.

Installation

The client can be installed independently of the MorphoCluster application using pip:

pip install morphocluster.lib

Command Line Interface (CLI)

(Re-)clustering

Usage: morphocluster cluster [OPTIONS] FEATURES_FNS... RESULT_FN

  (Re-)cluster.

Options:
  --tree PATH
  --min-cluster-size INTEGER
  --min-samples INTEGER
  --method [eom|leaf]           Leaf or excess-of-mass clustering. (Default:
                                leaf.)
  --sample-size INTEGER
  --pca INTEGER
  --init-tree / --no-init-tree  Initialize tree from dataset.
  --keep-unexplored FLOAT       Subsample unexplored data for clustering.
                                Can speed up clustering.         Number in
                                range (0,1).
  --help                        Show this message and exit.