ccc_circle_plot
Visualize cell-cell communication networks using a circular plot to analyze interactions between cell types, leveraging LIANA results for insights without coding.
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"
}