nichecompass.utils.generate_enriched_gp_info_plots

nichecompass.utils.generate_enriched_gp_info_plots(plot_label, model, sample_key, differential_gp_test_results_key, cat_key, cat_palette, n_top_enriched_gp_start_idx=0, n_top_enriched_gp_end_idx=10, feature_spaces=['latent'], n_top_genes_per_gp=3, n_top_peaks_per_gp=0, scale_omics_ft=False, save_figs=False, figure_folder_path='', file_format='png', spot_size=30.0)

Generate info plots of enriched gene programs. These show the enriched category, the gp activities, as well as the counts (or log normalized counts) of the top genes and/or peaks in a specified feature space.

Parameters:

  • plot_label (str) – Main label of the plots.

  • model (NicheCompass) – A trained NicheCompass model.

  • sample_key (str) – Key in ´adata.obs´ where the samples are stored.

  • differential_gp_test_results_key (str) – Key in ´adata.uns´ where the results of the differential gene program testing are stored.

  • cat_key (str) – Key in ´adata.obs´ where the categories that are used as colors for the enriched category plot are stored.

  • cat_palette (dict) – Dictionary of colors that are used to highlight the categories, where the category is the key of the dictionary and the color is the value.

  • n_top_enriched_gp_start_idx (int (default: 0)) – Number of top enriched gene program from which to start the creation of plots.

  • n_top_enriched_gp_end_idx (int (default: 10)) – Number of top enriched gene program at which to stop the creation of plots.

  • feature_spaces (list (default: ['latent'])) – List of feature spaces used for the info plots. Can be ´latent´ to use the latent embeddings for the plots, or it can be any of the samples stored in ´adata.obs[sample_key]´ to use the respective physical feature space for the plots.

  • n_top_genes_per_gp (int (default: 3)) – Number of top genes per gp to be considered in the info plots.

  • n_top_peaks_per_gp (int (default: 0)) – Number of top peaks per gp to be considered in the info plots. If ´>0´, requires the model to be trained inlcuding ATAC modality.

  • scale_omics_ft (bool (default: False)) – If ´True´, scale genes and peaks before plotting.

  • save_figs (bool (default: False)) – If ´True´, save the figures.

  • figure_folder_path (str (default: '')) – Folder path where the figures will be saved.

  • file_format (str (default: 'png')) – Format with which the figures will be saved.

  • spot_size (float (default: 30.0)) – Spot size used for the spatial plots.