stereo.algorithm.cell_cell_communication.PlotCellCellCommunication.ccc_sankey_plot#

PlotCellCellCommunication.ccc_sankey_plot(sender_cluster, receiver_cluster, homo_transfer=False, homogene_path=None, separator_cluster='|', separator_interaction='_', weighted_network_path=None, regulons=None, tfs=None, pct_expressed=0.05, max_path_length=4, width=600, height=880, out_path=None, receptor_tf_paths_out_path=None, res_key='cell_cell_communication')[source]#

Sankey-plot showing inter- and/or intra-cellular gene interaction. Left pillar is ligands, middle pillar receptors, # noqa right pillar TFs. The width of each band is the average expression of the two genes.

Parameters:

  • sender_cluster (str) – sender cell type

  • receiver_cluster (str) – receiver cell type

  • homo_transfer (bool) – If species is ‘MOUSE’ but database is ‘cellphonedb’ or ‘liana’, the gene names in the significant result have been transferred to ‘HUMAN’, we need to transfer them back in order to match the gene names in counts.

  • homogene_path (Optional[str]) – path to the file storing mouse-human homologous genes ralations.

  • separator_cluster (str) – separator used for cell cluster pairs

  • separator_interaction (str) – separator used for LR interaction

  • weighted_network_path (Optional[str]) – path to the weighted network

  • regulons (Union[str, Dict[str, list], None]) – path or dict to the spaGRN regulon output

  • tfs (Optional[List[str]]) – list of TFs used in the Sankey plot, if it is gave, the parameter regulons is ignored.

  • pct_expressed (float) – threshold used to detect expressed path between receptor and TF.

  • max_path_length (int) – the max path length between receptor and TF, paths longer than max_path_length is not considered as a potential pathway

  • width (int) – the figure width in pixels.

  • height (int) – the figure height in pixels.

  • out_path (Optional[str]) – the path to save the plot.

  • res_key (str) – the key which specifies the cell cell communication result in data.tl.result, defaults to ‘cell_cell_communication’. # noqa