External API: Preprocessing

scanpy.external.pp.harmony_integrate()

https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.harmony_integrate.html

integrate data sets (correct batch effect )

Notes:

• 1. before integration, all data sets should be store in the same AnnData object
• 2. the whole operation is about adjusting the principal components
• 3. this function should be run after performing PCA but before computing the neighbor graph (KNN)

scanpy.external.pp.harmony_integrate(adata, key=, basis=, adjusted_basis=)

• 1. key=: column of .obs to be used (the source of the batch effect)
• 2. basis=: the field name that PCA results were stored in .obsm; default='X_pca'
• 3. adjusted_basis=: the field name that the result will be stored in .obsm; default='X_pca_harmony'

Note: 整合后的结果存放在 .obsm['X_pca_harmony'] 中；维度与 .obsm['X_pca'] 相同