Readthedocs code examples II
This is the second round of adding code/output examples that are going to be displayed next to their respective function on the readthedocs site.
For none plotting functions please add a simple call and show the output. E.g. a table like adata.var
.
Functions that lack an example:
-
sctoolbox.tools.qc_filter.calculate_qc_metrics -
sctoolbox.tools.qc_filter.predict_cell_cycle -
sctoolbox.tools.qc_filter.estimate_doublets -
sctoolbox.tools.qc_filter.predict_sex -
sctoolbox.tools.qc_filter.automatic_thresholds -
sctoolbox.tools.qc_filter.thresholds_as_table -
sctoolbox.tools.qc_filter.get_thresholds_atac_wrapper -
sctoolbox.tools.qc_filter.get_keys -
sctoolbox.tools.highly_variable.annot_HVG -
sctoolbox.tools.highly_variable.get_variable_features -
sctoolbox.tools.norm_correct.atac_norm -
sctoolbox.tools.norm_correct.adata_normalize_total -
sctoolbox.tools.marker_genes.get_chromosome_genes -
sctoolbox.tools.marker_genes.label_genes -
sctoolbox.tools.marker_genes.add_gene_expression -
sctoolbox.tools.marker_genes.get_rank_genes_tables -
sctoolbox.tools.marker_genes.run_deseq2 -
sctoolbox.tools.marker_genes.score_genes -
sctoolbox.tools.celltype_annotation.add_cellxgene_annotation -
sctoolbox.tools.celltype_annotation.get_celltype_assignment -
sctoolbox.tools.celltype_annotation.run_scsa -
sctoolbox.tools.calc_overlap_pct.check_pct_fragments_in_promoters -
sctoolbox.tools.calc_overlap_pct.pct_fragments_in_promoters -
sctoolbox.tools.calc_overlap_pct.pct_fragments_overlap -
sctoolbox.tools.nucleosome_utils.moving_average -
sctoolbox.tools.nucleosome_utils.scale -
sctoolbox.tools.nucleosome_utils.calc_densities -
sctoolbox.tools.nucleosome_utils.call_peaks -
sctoolbox.tools.nucleosome_utils.filter_peaks -
sctoolbox.tools.nucleosome_utils.score_by_momentum -
sctoolbox.tools.nucleosome_utils.add_adapters -
sctoolbox.tools.nucleosome_utils.cross_point_shift -
sctoolbox.tools.nucleosome_utils.single_cwt_ov -
sctoolbox.tools.nucleosome_utils.score_by_cwt -
sctoolbox.tools.nucleosome_utils.density_plot -
sctoolbox.tools.nucleosome_utils.plot_single_momentum_ov -
sctoolbox.tools.nucleosome_utils.plot_wavl_ov -
sctoolbox.tools.nucleosome_utils.add_insertsize_metrics -
sctoolbox.tools.custom_celltype_annotation.annot_ct -
sctoolbox.tools.custom_celltype_annotation.modify_ct -
sctoolbox.tools.custom_celltype_annotation.show_tables -
sctoolbox.tools.custom_celltype_annotation.get_panglao -
sctoolbox.tools.custom_celltype_annotation.calc_ranks -
sctoolbox.tools.custom_celltype_annotation.get_cell_types -
sctoolbox.tools.custom_celltype_annotation.get_annotated_clusters -
sctoolbox.tools.multiomics.merge_anndata -
sctoolbox.tools.receptor_ligand.calculate_interaction_table -
sctoolbox.tools.receptor_ligand.interaction_violin_plot -
sctoolbox.tools.receptor_ligand.hairball -
sctoolbox.tools.receptor_ligand.interaction_progress -
sctoolbox.tools.receptor_ligand.connectionPlot -
sctoolbox.tools.receptor_ligand.get_interactions -
sctoolbox.tools.bam.bam_adata_ov -
sctoolbox.tools.bam.check_barcode_tag -
sctoolbox.tools.insertsize.add_insertsize -
sctoolbox.tools.peak_annotation.annotate_adata -
sctoolbox.tools.peak_annotation.annotate_narrowPeak -
sctoolbox.plotting.qc_filter.qc_violins -
sctoolbox.plotting.qc_filter.plot_insertsize -
sctoolbox.plotting.qc_filter.quality_violin -
sctoolbox.plotting.qc_filter.get_slider_thresholds -
sctoolbox.plotting.highly_variable.violin_HVF_distribution -
sctoolbox.plotting.highly_variable.scatter_HVF_distribution -
sctoolbox.plotting.embedding.plot_group_embeddings (example is broken) -
sctoolbox.plotting.embedding.compare_embeddings -
sctoolbox.plotting.embedding.umap_marker_overview -
sctoolbox.plotting.marker_genes.rank_genes_plot -
sctoolbox.plotting.marker_genes.grouped_violin (example broken?) -
sctoolbox.plotting.marker_genes.gene_expression_heatmap (example is broken) -
sctoolbox.plotting.marker_genes.group_heatmap -
sctoolbox.plotting.marker_genes.plot_differential_genes -
sctoolbox.plotting.velocity.pseudotime_heatmap -
sctoolbox.plotting.general.clustermap_dotplot -
sctoolbox.plotting.general.bidirectional_barplot -
sctoolbox.plotting.general.plot_obs_violin -
sctoolbox.plotting.general.plot_venn -
sctoolbox.utils.checker.check_module -
sctoolbox.utils.checker.is_str_numeric -
sctoolbox.utils.checker.validate_regions -
sctoolbox.utils.checker.format_adata_var -
sctoolbox.utils.checker.in_range -
sctoolbox.utils.checker.is_integer_array -
sctoolbox.utils.checker.check_columns -
sctoolbox.utils.checker.check_file_ending -
sctoolbox.utils.checker.is_regex -
sctoolbox.utils.io.get_temporary_filename -
sctoolbox.utils.logging.build_legend -
sctoolbox.utils.logging.get_user() -
sctoolbox.utils.logging.get_datetime() -
sctoolbox.utils.logging.add_uns_info -
sctoolbox.utils.logging.initialize_uns -
sctoolbox.utils.bioutils.pseudobulk_table -
sctoolbox.utils.bioutils.format_index -
sctoolbox.utils.bioutils.get_index_type -
sctoolbox.utils.bioutils.get_organism -
sctoolbox.utils.bioutils.gene_id_to_name -
sctoolbox.utils.bioutils.convert_id -
sctoolbox.utils.bioutils.unify_genes_column -
sctoolbox.utils.general.get_package_versions -
sctoolbox.utils.general.split_list -
sctoolbox.utils.general.split_list_size -
sctoolbox.utils.general.clean_flanking_strings -
sctoolbox.utils.general.longest_common_suffix -
sctoolbox.utils.general.remove_prefix -
sctoolbox.utils.general.remove_suffix -
sctoolbox.utils.general.sanitize_string -
sctoolbox.utils.tables.rename_categories -
sctoolbox.utils.tables.fill_na -
sctoolbox.utils.tables.table_zscore -
sctoolbox.utils.adata.get_adata_subsets -
sctoolbox.utils.adata.add_expr_to_obs -
sctoolbox.utils.adata.shuffle_cells
Edited by Jannik Luebke