Quick start

Status

  • Version 0.5.2 Fast model for NSBM (and PP).
  • Version 0.5.0 Introduces Planted Partition model
  • Version 0.4.2 Introduces functions to calculate cluster consistency.
  • Version 0.4.0 Some bugfixes and name change to schist
  • Version 0.3.1 It is possible to resume operatons on a previously modeled state (i.e. you can do two step analysis)
  • Version 0.3.0 Major changes in the way MCMC is performed. SBM is also available.
  • Version 0.2.5 extends scanpy.tools.draw_graph layouts to the ones available in graph-tool library
  • Version 0.2 The code for the interface is mature. It is also possible to read/write objects
  • Version 0.1 implements a working interface to graph-tool library for scanpy

How to use

Once schist has been installed, it can be used out of the box on scanpy objects:

from schist.inference import nested_model

nested_model(adata)

Once the MCMC has converged, the adata.obs object will contain additional columns for multiple levels, named nsbm_level_1, nsbm_level_2 and so on (by default up to nsbm_level_10).

Installation

The key component (graph-tool) is not available through pip and requires extra compilation by the user, refer to its installation page https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions. Note, however, that a conda package is available from conda-forge, that means you may install it (and schist dependencies) just issuing

conda create -n schist -c conda-forge -c bioconda numpy scipy anndata pandas 'graph-tool>=2.33' scanpy
conda activate schist

After that, schist can be installed from source:

git clone https://github.com/dawe/schist.git
cd schist
pip install .

Known issues

Saving objects

schist allows to return the NestedBlockState object in adata.uns[‘nsbm’][‘state’] slot. Unfortunately, this object cannot be dumped into .h5ad files by the sc.write() function. If you returned the state, e.g. for debugging, you should pop it out from your dataset before writing:

state = adata.uns['nsbm'].pop('state')
adata.write('myfile.h5ad')

## save the state separately
import pickle
with open('state.pkl', 'wb') as pkl_state:
        pickle.dump(state, pkl_state, 2)

Since version 0.2 it is possible to save AnnData objects like above simply issuing

schist.io.write(adata, prefix='myfile')

This will create two files: myfile.h5ad, containing the actual AnnData, and myfile.pkl containing the pickled state. With the same logic, assuming the two files are in the same place, issuing

adata = schist.io.read('myfile')

will read the .h5ad and the .pkl files and create the proper AnnData object