hucira.get_all_senders_and_receivers

hucira.get_all_senders_and_receivers#

hucira.get_all_senders_and_receivers(adata, cytokine_info, cytokine_list, celltype_colname='cell_type', sender_pvalue_threshold=0.1, receiver_mean_X_threshold=0)#

Compute cytokine sender and receiver statistics for a list of cytokines.

Best for visualization purposes (for plot_communication()).

Parameters:

  • adata (AnnData) – Query AnnData object.

  • cytokine_info (pandas.DataFrame) – Cytokine metadata containing receptor gene information, with columns "name", "gene", and "receptor gene".

  • cytokine_list (list of str) – List of cytokines to analyse. Should be present in cytokine_info.

  • celltype_colname (str) – Column name in adata.obs that stores cell types.

  • sender_pvalue_threshold (float) – Maximum p-value for a cell type to be considered a sender.

  • receiver_mean_X_threshold (float) – Minimum mean expression for a cell type to be considered a receiver.

Return type:

tuple[DataFrame, DataFrame]

Returns:

-df_src (DataFrame)

All cytokine signal senders.

-df_tgt (DataFrame)

All cytokine signal receivers.

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