U Åmœd^ ã@s6dZddlmZddlmZd eeeedœdd„Zd S) z< Use harmony to integrate cells from different experiments. é)ÚOptional)ÚAnnDataÚX_pcaÚ X_pca_harmony)ÚadataÚkeyÚbasisÚadjusted_basiscKsVz ddl}Wntk r(tdƒ‚YnX|j|j||j|f|Ž}|jj|j|<dS)a( Use harmonypy [Korunsky19]_ to integrate different experiments. Harmony [Korunsky19]_ is an algorithm for integrating single-cell data from multiple experiments. This function uses the python port of Harmony, ``harmonypy``, to integrate single-cell data stored in an AnnData object. As Harmony works by adjusting the principal components, this function should be run after performing PCA but before computing the neighbor graph, as illustrated in the example below. Parameters ---------- adata The annotated data matrix. key The name of the column in ``adata.obs`` that differentiates among experiments/batches. basis The name of the field in ``adata.obsm`` where the PCA table is stored. Defaults to ``'X_pca'``, which is the default for ``sc.tl.pca()``. adjusted_basis The name of the field in ``adata.obsm`` where the adjusted PCA table will be stored after running this function. Defaults to ``X_pca_harmony``. kwargs Any additional arguments will be passed to ``harmonypy.run_harmony()``. Returns ------- Updates adata with the field ``adata.obsm[obsm_out_field]``, containing principal components adjusted by Harmony such that different experiments are integrated. Example ------- First, load libraries and example dataset, and preprocess. >>> import scanpy as sc >>> import scanpy.external as sce >>> adata = sc.datasets.pbmc3k() >>> sc.pp.recipe_zheng17(adata) >>> sc.tl.pca(adata) We now arbitrarily assign a batch metadata variable to each cell for the sake of example, but during real usage there would already be a column in ``adata.obs`` giving the experiment each cell came from. >>> adata.obs['batch'] = 1350*['a'] + 1350*['b'] Finally, run harmony. Afterwards, there will be a new table in ``adata.obsm`` containing the adjusted PC's. >>> sce.pp.harmony_integrate(adata, 'batch') >>> 'X_pca_harmony' in adata.obsm True rNz2 please install harmonypy: pip install harmonypy)Ú harmonypyÚ ImportErrorZ run_harmonyZobsmZobsZZ_corrÚT)rrrr Úkwargsr Z harmony_out©rú^/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/external/pp/_harmony_integrate.pyÚharmony_integrate s C rN)rr)Ú__doc__ÚtypingrZanndatarÚstrrrrrrÚs  üü