ccc_dot_plot

Instructions

Visualize cell-cell communication interactions using a dotplot.

Input Schema

Name	Required	Description	Default
`cmap`	No	Colour map to use for plotting.	viridis
`colour`	No	Column in liana_res to define the colours of the dots.
`figure_size`	No	Figure x,y size.
`inverse_colour`	No	Whether to -log10 the colour column for plotting.
`inverse_size`	No	Whether to -log10 the size column for plotting.
`ligand_complex`	No	List of ligand complexes to filter the interactions to be plotted.
`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.
`receptor_complex`	No	List of receptor complexes to filter the interactions to be plotted.
`size`	No	Column in liana_res to define the size of the dots.
`size_range`	No	Define size range. Tuple of (min, max) integers.
`source_labels`	No	List of labels to use as source, the rest are filtered out.
`specificity_cutoff`	No	Specificity or p-value threshold for filtering results.
`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 dotplot visualization for cell-cell communication networks.",
  "properties": {
    "cmap": {
      "default": "viridis",
      "description": "Colour map to use for plotting.",
      "title": "Cmap",
      "type": "string"
    },
    "colour": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Column in liana_res to define the colours of the dots.",
      "title": "Colour"
    },
    "figure_size": {
      "default": [
        8,
        6
      ],
      "description": "Figure x,y size.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "number"
        },
        {
          "type": "number"
        }
      ],
      "title": "Figure Size",
      "type": "array"
    },
    "inverse_colour": {
      "default": false,
      "description": "Whether to -log10 the colour column for plotting.",
      "title": "Inverse Colour",
      "type": "boolean"
    },
    "inverse_size": {
      "default": false,
      "description": "Whether to -log10 the size column for plotting.",
      "title": "Inverse Size",
      "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"
    },
    "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"
    },
    "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"
    },
    "size": {
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Column in liana_res to define the size of the dots.",
      "title": "Size"
    },
    "size_range": {
      "default": [
        2,
        9
      ],
      "description": "Define size range. Tuple of (min, max) integers.",
      "maxItems": 2,
      "minItems": 2,
      "prefixItems": [
        {
          "type": "integer"
        },
        {
          "type": "integer"
        }
      ],
      "title": "Size Range",
      "type": "array"
    },
    "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 p-value threshold for filtering results.",
      "title": "Specificity Cutoff",
      "type": "number"
    },
    "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": {
      "default": "liana_res",
      "description": "Key in adata.uns that contains the LIANA results.",
      "title": "Uns Key",
      "type": "string"
    }
  },
  "title": "DotPlotModel",
  "type": "object"
}

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Input Schema

Input Schema (JSON Schema)

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