report

besca.tl.auto_annot.report(adata_pred, celltype, method, analysis_name, train_datasets, test_dataset, merge, use_raw=False, genes_to_use='all', remove_nonshared=False, clustering='leiden', asymmetric_matrix=True)[source]

reports basic metrics, produces confusion matrices and plots umap of prediction Writes out a csv file containing all accuracy and f1 scores. Writes normalized and absolute confusion matrices, as well as umap prediction comparisons to ./figures.

Parameters:

  • adata_pred (AnnData) – original adata object with ‘auto_annot’ column

  • celltype (str) – celltype column on which the prediction was performed

  • method (str) – method that was used for prediction.

  • analysis_name (str) – name of the analyis, used for writing files

  • train_datasets (list) – list of used training datasets

  • test_dataset (str) – name of test dataset

  • merge (str) – what merging was performed

  • use_raw (bool | default = False) – if anndata.raw was used

  • genes_to_use (list or string | default = ‘all’) – what geneset wsa used

  • remove_nonshared (`bool`|default = False) –

  • clustering (str | default = leiden) – clustering that was used in original analysis of testing set, needed for umap plotting

  • asymmetric_matrix (bool | default = True) – if False returns square confusion matrix, if True it only shows possible combinations

Return type:

0