U ÅmœdÀ ã@s,dZdZdZdZdZdZdZdZdZd Z d S) z8Shared docstrings for experimental function parameters. uuadata The annotated data matrix of shape `n_obs` × `n_vars`. Rows correspond to cells and columns to genes. a,theta The negative binomial overdispersion parameter `theta` for Pearson residuals. Higher values correspond to less overdispersion (`var = mean + mean^2/theta`), and `theta=np.Inf` corresponds to a Poisson model. clip Determines if and how residuals are clipped: * If `None`, residuals are clipped to the interval `[-sqrt(n_obs), sqrt(n_obs)]`, where `n_obs` is the number of cells in the dataset (default behavior). * If any scalar `c`, residuals are clipped to the interval `[-c, c]`. Set `clip=np.Inf` for no clipping. acheck_values If `True`, checks if counts in selected layer are integers as expected by this function, and return a warning if non-integers are found. Otherwise, proceed without checking. Setting this to `False` can speed up code for large datasets. zHlayer Layer to use as input instead of `X`. If `None`, `X` is used. zrsubset Inplace subset to highly-variable genes if `True` otherwise merely indicate highly variable genes. a÷n_top_genes Number of highly-variable genes to keep. Mandatory if `flavor='seurat_v3'` or `flavor='pearson_residuals'`. batch_key If specified, highly-variable genes are selected within each batch separately and merged. This simple process avoids the selection of batch-specific genes and acts as a lightweight batch correction method. Genes are first sorted by how many batches they are a HVG. If `flavor='pearson_residuals'`, ties are broken by the median rank (across batches) based on within-batch residual variance. chunksize If `flavor='pearson_residuals'`, this dertermines how many genes are processed at once while computing the residual variance. Choosing a smaller value will reduce the required memory. an_comps Number of principal components to compute in the PCA step. random_state Random seed for setting the initial states for the optimization in the PCA step. kwargs_pca Dictionary of further keyword arguments passed on to `scanpy.pp.pca()`. z~inplace If `True`, update `adata` with results. Otherwise, return results. See below for details of what is returned. zÁcopy If `True`, the function runs on a copy of the input object and returns the modified copy. Otherwise, the input object is modified direcly. Not compatible with `inplace=False`. N) Ú__doc__Z doc_adataZdoc_dist_paramsZdoc_check_valuesZ doc_layerZ doc_subsetZdoc_genes_batch_chunkZ doc_pca_chunkZ doc_inplaceZdoc_copy©rrúR/home/sam/Atlas/atlas_env/lib/python3.8/site-packages/scanpy/experimental/_docs.pyÚs