U md:!@sfddlmZddlmZmZmZmZmZmZddl Z ddl Z ddl mZddlmZddlmZddlmZdd lmZmZd d lmZmZd d lmZd d lmZzddlm Z Wn(e!k rGdddZ de _"YnXdddddddddeidddf eee#ej$eee%ee%fe%eeede&e&eee ee%efee%ee%e&eedddZ'dS))MappingProxyType)OptionalTupleSequenceTypeMappingAnyN)AnnData) natsorted)spmatrix)version) rename_groupsrestrict_adjacency)_utilslogging)Literal) _choose_graph)MutableVertexPartitionc@s eZdZdS)rN)__name__ __module__ __qualname__rrN/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/tools/_louvain.pyrsrzlouvain.VertexPartitionlouvainvtraagTF)rigraphrapids)adata resolution random_state restrict_to key_added adjacencyflavordirected use_weightspartition_typepartition_kwargs neighbors_keyobspcopyreturnc$Cst| } td}|dkr*| dk r*td| r6|n|}|dkrNt|| | }|dk rp|\}}t||||\}}|dkr|dkr|dk rtd|r|dkrd}|std t j ||d }|rt |j d t j}nd}|dkrld dl}| dkr|j} |dk r|| d <|r$|| d<t|jtdkrH||n|| d<td|j|| f| }n |j|d}t |j}n`|dkrd dl}d dl}||j}||j}|r|\}}|||f}t|t j r|j!}||}nd}|"}t#|dr |$|||n|%|||td|dk rV|j||d\}}n||\}}|&'ddg()}nf|dkrd dl*}d dl+} |"|}| ,|}!t j-t.|!t/d}|!0D]\}"}#|#||"<qntd|dk r|dkr|d7}t1||||||}t2j3|dt4t5t6t 7|d|j8|<i|j9d<t||d |j9dd!<tjd"|d#t.t 7|d$|d%d&| r|SdS)'uD Cluster cells into subgroups [Blondel08]_ [Levine15]_ [Traag17]_. Cluster cells using the Louvain algorithm [Blondel08]_ in the implementation of [Traag17]_. The Louvain algorithm has been proposed for single-cell analysis by [Levine15]_. This requires having ran :func:`~scanpy.pp.neighbors` or :func:`~scanpy.external.pp.bbknn` first, or explicitly passing a ``adjacency`` matrix. Parameters ---------- adata The annotated data matrix. resolution For the default flavor (``'vtraag'``) or for ```RAPIDS```, you can provide a resolution (higher resolution means finding more and smaller clusters), which defaults to 1.0. See “Time as a resolution parameter” in [Lambiotte09]_. random_state Change the initialization of the optimization. restrict_to Restrict the clustering to the categories within the key for sample annotation, tuple needs to contain ``(obs_key, list_of_categories)``. key_added Key under which to add the cluster labels. (default: ``'louvain'``) adjacency Sparse adjacency matrix of the graph, defaults to neighbors connectivities. flavor Choose between to packages for computing the clustering. ``'vtraag'`` is much more powerful, and the default. directed Interpret the ``adjacency`` matrix as directed graph? use_weights Use weights from knn graph. partition_type Type of partition to use. Only a valid argument if ``flavor`` is ``'vtraag'``. partition_kwargs Key word arguments to pass to partitioning, if ``vtraag`` method is being used. neighbors_key Use neighbors connectivities as adjacency. If not specified, louvain looks .obsp['connectivities'] for connectivities (default storage place for pp.neighbors). If specified, louvain looks .obsp[.uns[neighbors_key]['connectivities_key']] for connectivities. obsp Use .obsp[obsp] as adjacency. You can't specify both `obsp` and `neighbors_key` at the same time. copy Copy adata or modify it inplace. Returns ------- :obj:`None` By default (``copy=False``), updates ``adata`` with the following fields: ``adata.obs['louvain']`` (:class:`pandas.Series`, dtype ``category``) Array of dim (number of samples) that stores the subgroup id (``'0'``, ``'1'``, ...) for each cell. :class:`~anndata.AnnData` When ``copy=True`` is set, a copy of ``adata`` with those fields is returned. zrunning Louvain clusteringrNzD`partition_type` is only a valid argument when `flavour` is "vtraag">rrrz8`resolution` parameter has no effect for flavor "igraph"Fz using the undirected graph)r&weightrZresolution_parameterweightsz0.7.0seedz/ using the "louvain" package of Traag (2017))r/r add_adj_listz) using the "louvain" package of rapids)r Zvertex partitionZtaynaud)Zdtypez7`flavor` needs to be "vtraag" or "igraph" or "taynaud".rZ_RU)values categories)r r!paramsz finishedzfound z clusters and added z-, the cluster labels (adata.obs, categorical))timedeep):dictlogginfo ValueErrorr,rrwarningdebugrZget_igraph_from_adjacencynparrayesZastypeZfloat64rZRBConfigurationVertexPartitionr parse __version__Z set_rng_seedZfind_partitionZcommunity_multilevelZ membershipcudfcugraphZSeriesZindptrindicesZnonzero isinstancematrixA1ZGraphhasattrr1Zfrom_cudf_adjlistZ to_pandasZ sort_valuesZto_numpyZravelZnetworkx communityZbest_partitionZzeroslenintitemsrpdZ Categoricalr mapstruniqueZobsZuns)$rr r!r"r#r$r%r&r'r(r)r*r+r,startZ restrict_keyZrestrict_categoriesZrestrict_indicesgr/rpartgroupsrDrEoffsetsrFsourcestargetsZ louvain_parts_nxrKr2kvrrrrsR                             )(typesrtypingrrrrrrnumpyr?ZpandasrOZanndatar Znatsortr Z scipy.sparser packagingr Z_utils_clusteringrrrrr:Z_compatrrZlouvain.VertexPartitionr ImportErrorrfloatZ AnyRandomrQboolrrrrrs\