U md,@sdZddlmZmZmZddlmZddlmZddl m Z ddl m Z ddlmZdd lmZd Zdd d d ddddd d dd d eeedeed feeeeeeedefeeedeeeeeeeeedddZd S)z*Denoise high-dimensional data using MAGIC )UnionSequenceOptional)AnnData)version)logging)settings)Literal) AnyRandomz2.0NdexactZ euclideanF) knndecayknn_maxtn_pcasolverknn_dist random_staten_jobsverbosecopy) all_genespca_onlyauto)rZ approximate)adata name_listrrrrrrrrrrrreturnc  Kshzddlm}m}Wntk r0tdYn,Xt|ttks\tdtd|dtd}t |t t df}|r|d krt d | dkr| } n|s| st d |d | r| n|}| dkrtjn| } |f|||||||| | | d | j||d}tjd||dkrdndd|dkr:|j|jd<n | rL||_|}n||_|j|_| rd|SdS)a Markov Affinity-based Graph Imputation of Cells (MAGIC) API [vanDijk18]_. MAGIC is an algorithm for denoising and transcript recover of single cells applied to single-cell sequencing data. MAGIC builds a graph from the data and uses diffusion to smooth out noise and recover the data manifold. The algorithm implemented here has changed primarily in two ways compared to the algorithm described in [vanDijk18]_. Firstly, we use the adaptive kernel described in Moon et al, 2019 [Moon17]_ for improved stability. Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements. More information and bug reports `here `__. For help, visit . Parameters ---------- adata An anndata file with `.raw` attribute representing raw counts. name_list Denoised genes to return. The default `'all_genes'`/`None` may require a large amount of memory if the input data is sparse. Another possibility is `'pca_only'`. knn number of nearest neighbors on which to build kernel. decay sets decay rate of kernel tails. If None, alpha decaying kernel is not used. knn_max maximum number of nearest neighbors with nonzero connection. If `None`, will be set to 3 * `knn`. t power to which the diffusion operator is powered. This sets the level of diffusion. If 'auto', t is selected according to the Procrustes disparity of the diffused data. n_pca Number of principal components to use for calculating neighborhoods. For extremely large datasets, using n_pca < 20 allows neighborhoods to be calculated in roughly log(n_samples) time. If `None`, no PCA is performed. solver Which solver to use. "exact" uses the implementation described in van Dijk et al. (2018) [vanDijk18]_. "approximate" uses a faster implementation that performs imputation in the PCA space and then projects back to the gene space. Note, the "approximate" solver may return negative values. knn_dist recommended values: 'euclidean', 'cosine', 'precomputed' Any metric from `scipy.spatial.distance` can be used distance metric for building kNN graph. If 'precomputed', `data` should be an n_samples x n_samples distance or affinity matrix. random_state Random seed. Defaults to the global `numpy` random number generator. n_jobs Number of threads to use in training. All cores are used by default. verbose If `True` or an integer `>= 2`, print status messages. If `None`, `sc.settings.verbosity` is used. copy If true, a copy of anndata is returned. If `None`, `copy` is True if `genes` is not `'all_genes'` or `'pca_only'`. `copy` may only be False if `genes` is `'all_genes'` or `'pca_only'`, as the resultant data will otherwise have different column names from the input data. kwargs Additional arguments to `magic.MAGIC`. Returns ------- If `copy` is True, AnnData object is returned. If `subset_genes` is not `all_genes`, PCA on MAGIC values of cells are stored in `adata.obsm['X_magic']` and `adata.X` is not modified. The raw counts are stored in `.raw` attribute of AnnData object. Examples -------- >>> import scanpy as sc >>> import scanpy.external as sce >>> adata = sc.datasets.paul15() >>> sc.pp.normalize_per_cell(adata) >>> sc.pp.sqrt(adata) # or sc.pp.log1p(adata) >>> adata_magic = sce.pp.magic(adata, name_list=['Mpo', 'Klf1', 'Ifitm1'], knn=5) >>> adata_magic.shape (2730, 3) >>> sce.pp.magic(adata, name_list='pca_only', knn=5) >>> adata.obsm['X_magic'].shape (2730, 100) >>> sce.pp.magic(adata, name_list='all_genes', knn=5) >>> adata.X.shape (2730, 3451) r)MAGIC __version__zxPlease install magic package via `pip install --user git+git://github.com/KrishnaswamyLab/MAGIC.git#subdirectory=python`z!scanpy requires magic-impute >= vz (detected: vzN). Please update magic package via `pip install --user --upgrade magic-impute`zcomputing MAGICN>NrrzVInvalid string value for `name_list`: Only `'all_genes'` and `'pca_only'` are allowed.z]Can only perform MAGIC in-place with `name_list=='all_genes' or `name_list=='pca_only'` (got z). Consider setting `copy=True`) rrrrrrrrrr)Zgenesz finishedrz:added 'X_magic', PCA on MAGIC coordinates (adata.obsm))timedeepX_magic)magicr!r" ImportErrorrparse MIN_VERSIONlogginfo isinstancestrtype ValueErrorrr rZ fit_transformXZobsmraw)rrrrrrrrrrrrrkwargsr!r"startZ all_or_pcar&r5R/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/external/pp/_magic.pyr'srr        r')N)__doc__typingrrrZanndatar packagingrr#rr+Z _settingsr Z_compatr _utilsr r*r.intfloatboolr'r5r5r5r6sJ