sc_toolbox.tools.correlate_to_signature#

sc_toolbox.tools.correlate_to_signature(adata, marker, log_fc_threshold=0.7, cell_type='AT2 cells', cell_type_label='cell_type', log_fc_label='logfoldchange', gene_label='gene', use_raw=True)[source]#

Correlations Score (based on cell type signature (logFC)) - alternative to sc.tl.score

Parameters:

  • adata – AnnData object containing the data

  • marker (DataFrame) – Pandas DataFrame containing marker genes

  • log_fc_threshold (float) – Log fold change label

  • cell_type (str) – Cell type to calculate the correlation for

  • cell_type_label (str) – Label of all cell types in the AnnData object

  • log_fc_label (str) – Label of fold change in the AnnData object

  • gene_label (str) – Label of genes in the AnnData object

  • use_raw (bool) – Whether to use adata.raw.X

Returns:

List of correlations