CellCellCommunicationPlots¶

Visualization for cell-cell communication inference.

Input¶

• cccfile: The output file from CellCellCommunication

Output¶

• outdir: Default: {{in.cccfile | stem}}_plots.
  The output directory for the plots.
  

Environment Variables¶

• subset: An expression to pass to dplyr::filter() to subset the ccc data.
  
• magnitude: The column name in the data to use as the magnitude of the communication. By default, the second last column will be used.
  See li.mt.show_methods() for the available methods in LIANA. or https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html#Tileplot
• specificity: The column name in the data to use as the specificity of the communication.
  By default, the last column will be used. If the method doesn't have a specificity, set it to None.
  
• devpars (ns): The parameters for the plot.
  
  • res (type=int): Default: 100.
    The resolution of the plot
  • height (type=int): The height of the plot
  • width (type=int): The width of the plot
• more_formats (type=list): Default: [].
  The additional formats to save the plots.
  
• descr: Default: Cell-cell communication plot.
  The description of the plot.
  
• cases (type=json): Default: {}.
  The cases for the plots.
  The keys are the names of the cases and the values are the arguments for the plots. The arguments include the ones inherited from envs.
  
• <more>: Other arguments passed to scplotter::CCCPlot