Fetch a precompiled atlas landmarkΒΆ

In this example, we will map cells onto a custom atlas, using the Averages class:

import anndata
import northstar

# Initialize the class
af = northstar.AtlasFetcher()

# Get a list of the available landmarks
landmarks = af.list_atlases()

# Get one of them
atlas_sub = af.fetch_atlas(
    'Darmanis_2015',
    kind='subsample',
)

You can also fetch multiple atlases at once. They will be merged together. Because not all genes are present in all atlases, you can decide what to do for the genes that are missing from some atlases. In this example, we keep all genes and, for each atlas, we pad the missing genes with zeros.

import anndata
import northstar

# Initialize the class
af = northstar.AtlasFetcher()

# Get a list of the available landmarks
landmarks = af.list_atlases()

# Get two atlases (merged)
atlas_sub = af.fetch_multiple_atlases(
    ['Darmanis_2015', 'Enge_2017'],
    kind='subsample',
    join='union',
)

Note

The atlas landmark in outpt is an instance of anndata.AnnData, with genes as rows and cells or cell types as colums.