Using Subsample with a precomputed atlas

In this example, we will map cells from human brain tumors (glioblastoma) onto an existing brain atlas in our precompiled atlas landmarks.

import anndata
import northstar

# Read in the GBM data to be annotated
# Here we assume it's a loom file, but
# of course it can be whatever format
newdata = anndata.read_loom('...')

# Prepare the classifier
# We exclude the fetal cells to focus
# on adult tissue. To keep the fetal
# cells, just take away the _nofetal
model = northstar.Subsample(
    atlas='Darmanis_2015_nofetal',
)

# Run the classification
model.fit(newdata)

# Get the inferred cell types
cell_types_newdata = model.membership

# Get UMAP coordinates of the atlas
# and new data (joint embedding)
embedding = model.embed('umap')