AnnDictionary

This module contains adata_dict wrappers for functions in anndict.

remove_genes_adata_dict(adata, genes_to_remove)	Remove specified genes from an AnnData object in-place.
ai_annotate_biological_process_adata_dict(...)	Annotate biological processes based on the top n marker genes for each cluster.
simplify_var_index_adata_dict(adata, column, ...)	Simplifies gene names in the index of the AnnData object's var attribute based on a boolean column, and stores the result in a new column using the map_gene_labels_to_simplified_set().
ensure_label_consistency_adata_dict(adata, cols)	Wrapper function to ensure label consistency across specified columns in an AnnData object.
simplify_obs_column_adata_dict(adata, ...[, ...])	Simplifies labels in the specified column of the AnnData object and stores the result in a new column using map_cell_type_labels_to_simplified_set().
create_label_hierarchy_adata_dict(adata, ...)	Create a hierarchy of simplified labels based on a given column in AnnData.
ai_annotate_cell_type_adata_dict(adata, ...)	Annotate cell types based on the top marker genes for each cluster.
ai_compare_cell_type_labels_pairwise_adata_dict(...)	Compare cell type labels by finding unique combinations between labels in cols1 and cols2, applying the comparison, and mapping the results back to adata.obs.
ai_annotate_cell_sub_type_adata_dict(adata, ...)	Annotate cell subtypes using an LLM.
ai_determine_leiden_resolution_adata_dict(...)	Adjusts the Leiden clustering resolution of an AnnData object based on LLM feedback.
harmony_label_transfer_adata_dict(...)	Perform Harmony integration and transfer labels from origin_adata to destination_adata.
plot_sankey_adata_dict(adata, cols[, params])	Generate a Sankey diagram from the specified columns in adata.obs.
save_sankey_adata_dict(plot, filename[, adt_key])	Save a Holoviews Sankey plot as an SVG file.
plot_grouped_average_adata_dict(adata, ...)	Plots the average values specified in label_value across each group of label_keys in an AnnData object.
plot_label_changes_adata_dict(adata, ...[, ...])	Plot the changes between true and predicted labels in an AnnData object.
plot_confusion_matrix_adata_dict(adata, ...)	Plots a confusion matrix from an AnnData object, with optional row and column colors.
summarize_metadata_adata_dict(adata, cols)	Generate a summary for specified metadata column(s) in adata.
display_html_summary_adata_dict(summary_dict)	Display separate HTML tables for each metadata category in the summary dictionary, arranging up to three tables in a row before starting a new line.
pca_density_adata_dict(adata[, use_layer, ...])	Filters pca_density_filter() that accepts AnnData as input.