API

import scanvi_explainer

SCANVIDeep

scanvi_deep.SCANVIDeep

SCANVIDeep is an extension of DeepExplainer [Lundberg and Lee, 2017] for models trained using SCANVI [Xu et al., 2021].

SCANVIBoostrapper

scanvi_bootstrapper.SCANVIBoostrapper

Utilities

utils.get_labels_key	Retrieve key from .obs with labels used to train the classifier
utils.get_layer_key	Retrieve layers key of counts which the model was trained on
utils.train_test_group_split	Function to split anndata object 80/20 per group in format required for SCANVIDeep explainer.

Plots

plots.feature_plot

Prints feature contribution (absolute mean SHAP value) for each cell type (top 10).