sc_toolbox.tools.extended_marker_table#

sc_toolbox.tools.extended_marker_table(adata, qval_thresh=0.05, cell_type_label='cell_type', gene_ranks_key='rank_genes_groups')[source]#

Generates an extended marker table with cell types and percentages of expressed cell types per cluster.

Run scanpy.tl.rank_genes_groups before using this function.

Parameters:

  • adata (AnnData) – AnnData object containing ranked genes

  • qval_thresh (float) – Threshold to filter the log fold change for

  • cell_type_label (str) – Label containing all cell types

  • gene_ranks_key (str) – Key for the ranked gene groups (generated by sc.tl.rank_genes_groups)

Returns:

A Pandas DataFrame