dotools_py.dt.example_visium_processed

dotools_py.dt.example_visium_processed()

Load example Visium datasets processed.

Loads a reduced version of the example datasets from Visium used in the tutorial of the package.

Return type:

AnnData

Returns:

Returns an AnnData object processed with 1046 cells and 1000 genes.

Example

>>> import dotools_py as do
>>> adata = do.dt.example_visium_processed()
>>> adata
AnnData object with n_obs × n_vars = 1046 × 1000
obs: 'in_tissue', 'array_row', 'array_col', 'batch', 'condition', 'tissue', 'n_genes_by_counts',
     'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt',
     'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'total_counts_hb',
     'log1p_total_counts_hb', 'pct_counts_hb', 'n_genes', 'n_counts', 'leiden'
var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'highly_variable_nbatches',
     'highly_variable_intersection'
uns: 'hvg', 'leiden_colors', 'log1p', 'neighbors', 'spatial', 'spatial_neighbors', 'umap'
obsm: 'X_pca', 'X_umap', 'spatial'
layers: 'counts', 'logcounts'
obsp: 'connectivities', 'distances', 'spatial_connectivities', 'spatial_distances'