Reference documentation ======================== Documentation for module functions (for developers) assign.py --------- ``poppunk_assign`` main function .. automodule:: PopPUNK.assign :members: bgmm.py -------- Functions used to fit the mixture model to a database. Access using :class:`~PopPUNK.models.BGMMFit`. .. automodule:: PopPUNK.bgmm :members: dbscan.py --------- Functions used to fit DBSCAN to a database. Access using :class:`~PopPUNK.models.DBSCANFit`. .. automodule:: PopPUNK.dbscan :members: mandrake.py ----------- .. automodule:: PopPUNK.mandrake :members: models.py --------- .. automodule:: PopPUNK.models :members: network.py ---------- Functions used to construct the network, and update with new queries. Main entry point is :func:`~PopPUNK.network.constructNetwork` for new reference databases, and :func:`~PopPUNK.network.findQueryLinksToNetwork` for querying databases. .. automodule:: PopPUNK.network :members: refine.py --------- Functions used to refine an existing model. Access using :class:`~PopPUNK.models.RefineFit`. .. automodule:: PopPUNK.refine :members: plot.py -------- .. automodule:: PopPUNK.plot :members: sparse_mst.py ------------- .. automodule:: PopPUNK.sparse_mst :members: sketchlib.py ------------ .. automodule:: PopPUNK.sketchlib :members: utils.py -------- .. automodule:: PopPUNK.utils :members: visualise.py ------------ ``poppunk_visualise`` main function .. automodule:: PopPUNK.visualise :members: web.py -------- Functions used by the web API to convert a sketch to an h5 database, then generate visualisations and post results to PopPUNK-web. .. automodule:: PopPUNK.web :members: