sc_toolbox.tools.automated_marker_annotation#

sc_toolbox.tools.automated_marker_annotation(adata, organism, tissue, marker_file, key='rank_genes_groups', normalize='reference', p_value=0.05, log_fold_change=2)[source]#

Calculates a marker gene overlap based on pre-existing annotations.

Currently supported marker files:

Organism

Tissue

Marker File

Mouse

Lung

lung_particle_markers.txt

Human

NA
Parameters:

  • adata (AnnData) – AnnData object containing ranked genes

  • organism (str) – Currently supported: ‘mouse’

  • tissue (str) – Currently supported: ‘lung’

  • marker_file (str) – Name of the marker file to be used - refer to table

  • key (str) – Key of ranked genes in adata (default: ‘rank_genes_groups’)

  • normalize (Optional[Literal['reference', 'data']]) – Normalization option for the marker gene overlap output (default: ‘reference’)

  • p_value (float) – p-value threshold for existing marker genes (default: 0.05)

  • log_fold_change (float) – log fold change threshold for existing marker genes (default: 2)

Returns:

Pandas DataFrame of overlapping genes. Visualize with a Seaborn Heatmap