API

Datasets

Class to contain datasets, sample/cell metadata, cNMF parameters, and cNMF results:

mosaicmpi.Dataset(adata[, force_migrate])

Creates a Dataset object from an anndata.AnnData object.

These can be made from from pandas data matrices or imported from AnnData files/objects.

mosaicmpi.Dataset.from_df(data, is_normalized)	Creates a Dataset object from a pandas DataFrame.
mosaicmpi.Dataset.from_h5ad(h5ad_file[, ...])	Creates a Dataset object from an AnnData-compatible .h5ad file.
mosaicmpi.Dataset.from_anndata(adata[, ...])	Creates a Dataset object from an anndata.AnnData object.

Integration of programs across resolutions and datasets

To identify program anchors, create an Integration object from one or more datasets. Then, create a Network object from the Integration object.

mosaicmpi.Integration(datasets[, ...])	Integrate multiple datasets together.
mosaicmpi.Network(integration[, ...])	Create a program network from an Integration object.

Visualizing MosaicMPI integrations

Class to enable consistent color palettes for metadata categories, program communities, and datasets.

mosaicmpi.Colors([metadata_colors, ...])

Visually-distinct colors can be auto-generated from Dataset, Integration, or Network objects:

mosaicmpi.Colors.from_dataset(dataset[, ...])
mosaicmpi.Colors.from_integration(integration)
mosaicmpi.Colors.from_network(network[, ...])

Functions to create plots from Dataset, Integration, and Network objects are in the plots module:

mosaicmpi.plots

Complete API Reference

mosaicmpi