ccc_dot_plot
Generate a dotplot to visualize cell-cell communication interactions, filtering and customizing results by specificity, size, color, and specific cell labels for clearer biological insights.
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"
}