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.
    You can have a special plot_type "table" to generate a table for the ccc data to save as a text file and show in the report.
    If no cases are given, a default case will be used, with the key Cell-Cell Communication.
  • <more>: Other arguments passed to scplotter::CCCPlot

Examples

Network Plot

[CellCellCommunicationPlots.envs.cases."Cell-Cell Communication Network"]
plot_type = "network"
legend-position = "none"
theme = "theme_blank"
theme_args = {add_coord = false}

Network Plot

Circos Plot

Circos Plot

Heatmap Plot

Heatmap Plot

Cell-Cell Communication Interaction (Box Plot)

[CellCellCommunicationPlots.envs.cases."Cell-Cell Communication Interaction (Box Plot)"]
plot_type = "box"
x_text_angle = 90
method = "interaction"

Box Plot