adataviz package

Submodules

• adataviz.adata module
  • AnnDataCollection
    • AnnDataCollection.from_files()
    • AnnDataCollection.read()
    • AnnDataCollection.update_paths()
  • AnnDataView
    • AnnDataView.to_memory()
  • is_annadatacollection()
  • main()
  • test_subset()
• adataviz.plotting module
  • get_boxplot_data()
  • get_genes_mean_frac()
  • has_stats()
  • interactive_boxplot()
  • interactive_dotHeatmap()
  • interactive_embedding()
  • pieplot()
  • plot_categorical()
  • plot_gene()
  • plot_genes()
  • plot_interacrive_boxplot_from_stats()
  • plot_interactive_boxlot_from_data()
  • plot_pseudotime()
  • show_fig()
  • stacked_barplot()
  • stacked_violinplot()
  • use_scientific_style()
• adataviz.tools module
  • cal_stats()
  • cal_tpm()
  • composition()
  • downsample_adata()
  • export_pseudobulk_adata()
  • get_color_palette()
  • get_markers()
  • get_markers_worker()
  • get_obs()
  • load_adata()
  • load_color_palette()
  • load_obs()
  • merge_adata_regions()
  • normalize_adata()
  • prepare_color_palette()
  • scrna2pseudobulk()
  • stat_pseudobulk()
  • taxonomy()
• adataviz.utils module
  • TextWithCircleHandler
    • TextWithCircleHandler.create_artists()
  • categorical_scatter()
  • continuous_scatter()
  • density_contour()
  • despine()
  • df2stdout()
  • get_brain_region_structure()
  • get_cmap()
  • level_one_palette()
  • mpl_style()
  • normalize_mc_by_cell()
  • parse_gtf()
  • parse_json()
  • plot_cmap_legend()
  • plot_color_dict_legend()
  • plot_marker_legend()
  • plot_text_legend()
  • prepare_color_palette()
  • read_google_sheet()
  • serialize()
  • tight_hue_range()
  • zoom_ax()
  • zoom_min_max()

Module contents

adataviz.adataviz(command=None)

Usage: adataviz command [options]

Available commands are:

plot: plot adata tool: Other tools

Parameters:

command – choice from [‘plot’, ‘tool’]

adataviz.main()