ccc_circle_plot

Instructions

Visualize cell-cell communication network using a circular plot.

Input Schema

Name	Required	Description	Default
`edge_alpha`	No	The transparency of the edges.
`edge_arrow_size`	No	The size of the arrow.
`edge_width_scale`	No	The scale of the edge width.
`figure_size`	No	Figure x,y size.
`groupby`	No	Key to be used for grouping or clustering cells.
`inverse_score`	No	Whether to invert the score. If True, the score will be -log10(score).
`ligand_complex`	No	List of ligand complexes to filter the interactions to be plotted.
`mask_mode`	No	The mode of the mask: 'or' to include source or target, 'and' to include source and target.	or
`node_alpha`	No	The transparency of the nodes.
`node_label_alpha`	No	The transparency of the node label.
`node_label_offset`	No	The offset of the node label.
`node_label_size`	No	The size of the node label.
`node_size_scale`	No	The scale of the node size.
`orderby`	No	If top_n is not None, order the interactions by this column.
`orderby_absolute`	No	If top_n is not None, whether to order by the absolute value of the orderby column.
`orderby_ascending`	No	If top_n is not None, specify how to order the interactions.
`pivot_mode`	No	The mode of the pivot table: 'counts' for number of connections, 'mean' for mean of score values.	counts
`receptor_complex`	No	List of receptor complexes to filter the interactions to be plotted.
`score_key`	No	Column name of the score in liana_res. If None, the score is inferred from the method.
`source_key`	No	Column name of the sender/source cell types in liana_res.	source
`source_labels`	No	List of labels to use as source, the rest are filtered out.
`specificity_cutoff`	No	specificity or pval threshold for filtering results.
`target_key`	No	Column name of the receiver/target cell types in liana_res.	target
`target_labels`	No	List of labels to use as target, the rest are filtered out.
`top_n`	No	Top N entities to plot.
`uns_key`	No	Key in adata.uns that contains the LIANA results.	liana_res

Input Schema (JSON Schema)

{
  "description": "Input schema for LIANA's circle_plot visualization for cell-cell communication networks.",
  "properties": {
    "edge_alpha": {
      "default": 0.5,
      "description": "The transparency of the edges.",
      "title": "Edge Alpha",
      "type": "number"
    },
    "edge_arrow_size": {
      "default": 10,
      "description": "The size of the arrow.",
      "title": "Edge Arrow Size",
      "type": "integer"
    },
    "edge_width_scale": {
      "default": [
        1,
        5
      ],
      "description": "The scale of the edge width.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "number"
        },
        {
          "type": "number"
        }
      ],
      "title": "Edge Width Scale",
      "type": "array"
    },
    "figure_size": {
      "default": [
        5,
        5
      ],
      "description": "Figure x,y size.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "number"
        },
        {
          "type": "number"
        }
      ],
      "title": "Figure Size",
      "type": "array"
    },
    "groupby": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Key to be used for grouping or clustering cells.",
      "title": "Groupby"
    },
    "inverse_score": {
      "default": false,
      "description": "Whether to invert the score. If True, the score will be -log10(score).",
      "title": "Inverse Score",
      "type": "boolean"
    },
    "ligand_complex": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of ligand complexes to filter the interactions to be plotted.",
      "title": "Ligand Complex"
    },
    "mask_mode": {
      "default": "or",
      "description": "The mode of the mask: 'or' to include source or target, 'and' to include source and target.",
      "enum": [
        "and",
        "or"
      ],
      "title": "Mask Mode",
      "type": "string"
    },
    "node_alpha": {
      "default": 1,
      "description": "The transparency of the nodes.",
      "title": "Node Alpha",
      "type": "number"
    },
    "node_label_alpha": {
      "default": 0.7,
      "description": "The transparency of the node label.",
      "title": "Node Label Alpha",
      "type": "number"
    },
    "node_label_offset": {
      "default": [
        0.1,
        -0.2
      ],
      "description": "The offset of the node label.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "number"
        },
        {
          "type": "number"
        }
      ],
      "title": "Node Label Offset",
      "type": "array"
    },
    "node_label_size": {
      "default": 8,
      "description": "The size of the node label.",
      "title": "Node Label Size",
      "type": "integer"
    },
    "node_size_scale": {
      "default": [
        100,
        400
      ],
      "description": "The scale of the node size.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "number"
        },
        {
          "type": "number"
        }
      ],
      "title": "Node Size Scale",
      "type": "array"
    },
    "orderby": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If top_n is not None, order the interactions by this column.",
      "title": "Orderby"
    },
    "orderby_absolute": {
      "default": false,
      "description": "If top_n is not None, whether to order by the absolute value of the orderby column.",
      "title": "Orderby Absolute",
      "type": "boolean"
    },
    "orderby_ascending": {
      "anyOf": [
        {
          "type": "boolean"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "If top_n is not None, specify how to order the interactions.",
      "title": "Orderby Ascending"
    },
    "pivot_mode": {
      "default": "counts",
      "description": "The mode of the pivot table: 'counts' for number of connections, 'mean' for mean of score values.",
      "enum": [
        "counts",
        "mean"
      ],
      "title": "Pivot Mode",
      "type": "string"
    },
    "receptor_complex": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of receptor complexes to filter the interactions to be plotted.",
      "title": "Receptor Complex"
    },
    "score_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Column name of the score in liana_res. If None, the score is inferred from the method.",
      "title": "Score Key"
    },
    "source_key": {
      "default": "source",
      "description": "Column name of the sender/source cell types in liana_res.",
      "title": "Source Key",
      "type": "string"
    },
    "source_labels": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of labels to use as source, the rest are filtered out.",
      "title": "Source Labels"
    },
    "specificity_cutoff": {
      "default": 0.05,
      "description": "specificity or pval threshold for filtering results. ",
      "title": "Specificity Cutoff",
      "type": "number"
    },
    "target_key": {
      "default": "target",
      "description": "Column name of the receiver/target cell types in liana_res.",
      "title": "Target Key",
      "type": "string"
    },
    "target_labels": {
      "anyOf": [
        {
          "items": {
            "type": "string"
          },
          "type": "array"
        },
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "List of labels to use as target, the rest are filtered out.",
      "title": "Target Labels"
    },
    "top_n": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Top N entities to plot.",
      "title": "Top N"
    },
    "uns_key": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": "liana_res",
      "description": "Key in adata.uns that contains the LIANA results.",
      "title": "Uns Key"
    }
  },
  "title": "CirclePlotModel",
  "type": "object"
}

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Input Schema

Input Schema (JSON Schema)

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