pl_scatter
Generate scatter plots to visualize relationships between two variables in single-cell RNA sequencing data. Customize plots with color maps, annotations, and layout adjustments for clear data insights.
Instructions
Plot a scatter plot of two variables, Scatter plot along observations or variables axes.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| alpha | No | Alpha value for the plot. | |
| basis | No | Basis to use for embedding. | |
| color | No | Keys for annotations of observations/cells or variables/genes, or a hex color specification. | |
| color_map | No | Color map to use for continuous variables. | |
| components | No | For instance, ['1,2', '2,3']. To plot all available components use components='all'. | |
| figsize | No | Figure size. Format is (width, height). | |
| groups | No | Restrict to a few categories in categorical observation annotation. | |
| layers | No | Use the layers attribute of adata if present: specify the layer for x, y and color. | |
| left_margin | No | Adjust the width of the left margin. | |
| legend_fontoutline | No | Line width of the legend font outline in pt. | |
| legend_fontsize | No | Numeric size in pt or string describing the size. | |
| legend_fontweight | No | Legend font weight. A numeric value in range 0-1000 or a string. | bold |
| legend_loc | No | Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter. | right margin |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| projection | No | Projection of plot. | 2d |
| right_margin | No | Adjust the width of the right margin. | |
| sort_order | No | For continuous annotations used as color parameter, plot data points with higher values on top of others. | |
| use_raw | No | Whether to use raw attribute of adata. Defaults to True if .raw is present. | |
| vcenter | No | The value representing the center of the color scale. | |
| vmax | No | The value representing the upper limit of the color scale. | |
| vmin | No | The value representing the lower limit of the color scale. | |
| x | No | x coordinate. | |
| y | No | y coordinate. |
Input Schema (JSON Schema)
{
"description": "Input schema for the enhanced scatter plotting tool.",
"properties": {
"alpha": {
"anyOf": [
{
"maximum": 1,
"minimum": 0,
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Alpha value for the plot.",
"title": "Alpha"
},
"basis": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Basis to use for embedding.",
"title": "Basis"
},
"color": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Keys for annotations of observations/cells or variables/genes, or a hex color specification.",
"title": "Color"
},
"color_map": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Color map to use for continuous variables.",
"title": "Color Map"
},
"components": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "For instance, ['1,2', '2,3']. To plot all available components use components='all'.",
"title": "Components"
},
"figsize": {
"anyOf": [
{
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "number"
},
{
"type": "number"
}
],
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Figure size. Format is (width, height).",
"title": "Figsize"
},
"groups": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Restrict to a few categories in categorical observation annotation.",
"title": "Groups"
},
"layers": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Use the layers attribute of adata if present: specify the layer for x, y and color.",
"title": "Layers"
},
"left_margin": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Adjust the width of the left margin.",
"title": "Left Margin"
},
"legend_fontoutline": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Line width of the legend font outline in pt.",
"title": "Legend Fontoutline"
},
"legend_fontsize": {
"anyOf": [
{
"type": "integer"
},
{
"type": "number"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Numeric size in pt or string describing the size.",
"title": "Legend Fontsize"
},
"legend_fontweight": {
"anyOf": [
{
"type": "integer"
},
{
"type": "string"
}
],
"default": "bold",
"description": "Legend font weight. A numeric value in range 0-1000 or a string.",
"title": "Legend Fontweight"
},
"legend_loc": {
"default": "right margin",
"description": "Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter.",
"title": "Legend Loc",
"type": "string"
},
"palette": {
"anyOf": [
{
"type": "string"
},
{
"items": {
"type": "string"
},
"type": "array"
},
{
"additionalProperties": {
"type": "string"
},
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Colors to use for plotting categorical annotation groups.",
"title": "Palette"
},
"projection": {
"default": "2d",
"description": "Projection of plot.",
"enum": [
"2d",
"3d"
],
"title": "Projection",
"type": "string"
},
"right_margin": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Adjust the width of the right margin.",
"title": "Right Margin"
},
"sort_order": {
"default": true,
"description": "For continuous annotations used as color parameter, plot data points with higher values on top of others.",
"title": "Sort Order",
"type": "boolean"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether to use raw attribute of adata. Defaults to True if .raw is present.",
"title": "Use Raw"
},
"vcenter": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
},
{
"items": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
}
]
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "The value representing the center of the color scale.",
"title": "Vcenter"
},
"vmax": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
},
{
"items": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
}
]
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "The value representing the upper limit of the color scale.",
"title": "Vmax"
},
"vmin": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
},
{
"items": {
"anyOf": [
{
"type": "string"
},
{
"type": "number"
}
]
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "The value representing the lower limit of the color scale.",
"title": "Vmin"
},
"x": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "x coordinate.",
"title": "X"
},
"y": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "y coordinate.",
"title": "Y"
}
},
"title": "EnhancedScatterModel",
"type": "object"
}