adata_predict

besca.tl.auto_annot.adata_predict(classifier, scaler, adata_pred, adata_orig, threshold=0)[source]

predicts on testing set using trained classifier

Parameters:

  • test_path (string) – path of test dataset

  • test_dataset (string) – name of test dataset

  • adata_orig (AnnData) – Test dataset can also be provided as an anndata object. It is different from adata_pred in that it has not undergone scanorama merging.

  • classifier (sklearn object) – trained classifier of chosen type

  • scaler (sklearn.preprocessing.StandardScaler) – scaler fit to training dataset

  • adata_pred (AnnData) – Preprocessed anndata object containing testing dataset.

  • threshold (float | default = 0) – value between 0 and 1, used for classifying into unknowns

Returns:

Original anndata object with annotation added as column

Return type:

AnnData