pl_embedding
Generate scatter plots for user-specified embedding basis (e.g., UMAP, t-SNE) to visualize single-cell RNA sequencing data, with customizable parameters for color, size, and annotation.
Instructions
Scatter plot for user specified embedding basis (e.g. umap, tsne, etc).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| add_outline | No | Add outline to scatter plot points. | |
| arrows | No | Show arrows. | |
| arrows_kwds | No | Passed to matplotlib's quiver function for drawing arrows. | |
| basis | Yes | Name of the obsm basis to use. | |
| cmap | No | Color map to use for continuous variables. Overrides color_map. | |
| color | No | Keys for annotations of observations/cells or variables/genes. | |
| color_map | No | Color map to use for continuous variables. | |
| colorbar_loc | No | Location of the colorbar. | right |
| components | No | For instance, ['1,2', '2,3']. To plot all available components use components='all'. | |
| dimensions | No | 0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)]. | |
| edges | No | Show edges between nodes. | |
| edges_color | No | Color of edges. | grey |
| edges_width | No | Width of edges. | |
| figsize | No | Figure size. Format is (width, height). | |
| frameon | No | Draw a frame around the scatter plot. | |
| gene_symbols | No | Column name in .var DataFrame that stores gene symbols. | |
| groups | No | Restrict to a few categories in categorical observation annotation. | |
| hspace | No | Height space between panels. | |
| layer | No | Name of the AnnData object layer that wants to be plotted. | |
| 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 |
| marker | No | Matplotlib marker style for points. | . |
| mask_obs | No | A boolean array or a string mask expression to subset observations. | |
| na_color | No | Color to use for null or masked values. | lightgray |
| na_in_legend | No | Whether to include null values in the legend. | |
| ncols | No | Number of columns for multiple plots. | |
| neighbors_key | No | Where to look for neighbors connectivities. | |
| outline_color | No | Color of the outline for highlighted points. | |
| outline_width | No | Width of the outline for highlighted points. | |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| projection | No | Projection of plot. | 2d |
| scale_factor | No | Scale factor for the plot. | |
| size | No | Point size. If None, is automatically computed. | |
| sort_order | No | For continuous annotations used as color parameter, plot data points with higher values on top of others. | |
| title | No | Title for the plot. | |
| use_raw | No | Use .raw attribute of adata for coloring with gene expression. | |
| 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. | |
| wspace | No | Width space between panels. |
Input Schema (JSON Schema)
{
"description": "Input schema for the embedding plotting tool.",
"properties": {
"add_outline": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": false,
"description": "Add outline to scatter plot points.",
"title": "Add Outline"
},
"arrows": {
"default": false,
"description": "Show arrows.",
"title": "Arrows",
"type": "boolean"
},
"arrows_kwds": {
"anyOf": [
{
"additionalProperties": true,
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Passed to matplotlib's quiver function for drawing arrows.",
"title": "Arrows Kwds"
},
"basis": {
"description": "Name of the obsm basis to use.",
"title": "Basis",
"type": "string"
},
"cmap": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Color map to use for continuous variables. Overrides color_map.",
"title": "Cmap"
},
"color": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Keys for annotations of observations/cells or variables/genes.",
"title": "Color"
},
"color_map": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Color map to use for continuous variables.",
"title": "Color Map"
},
"colorbar_loc": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": "right",
"description": "Location of the colorbar.",
"title": "Colorbar Loc"
},
"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"
},
"dimensions": {
"anyOf": [
{
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "integer"
},
{
"type": "integer"
}
],
"type": "array"
},
{
"items": {
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "integer"
},
{
"type": "integer"
}
],
"type": "array"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)].",
"title": "Dimensions"
},
"edges": {
"default": false,
"description": "Show edges between nodes.",
"title": "Edges",
"type": "boolean"
},
"edges_color": {
"anyOf": [
{
"type": "string"
},
{
"items": {
"type": "number"
},
"type": "array"
},
{
"items": {
"type": "string"
},
"type": "array"
}
],
"default": "grey",
"description": "Color of edges.",
"title": "Edges Color"
},
"edges_width": {
"default": 0.1,
"description": "Width of edges.",
"title": "Edges Width",
"type": "number"
},
"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"
},
"frameon": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Draw a frame around the scatter plot.",
"title": "Frameon"
},
"gene_symbols": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Column name in .var DataFrame that stores gene symbols.",
"title": "Gene Symbols"
},
"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"
},
"hspace": {
"default": 0.25,
"description": "Height space between panels.",
"title": "Hspace",
"type": "number"
},
"layer": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Name of the AnnData object layer that wants to be plotted.",
"title": "Layer"
},
"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"
},
"marker": {
"anyOf": [
{
"type": "string"
},
{
"items": {
"type": "string"
},
"type": "array"
}
],
"default": ".",
"description": "Matplotlib marker style for points.",
"title": "Marker"
},
"mask_obs": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "A boolean array or a string mask expression to subset observations.",
"title": "Mask Obs"
},
"na_color": {
"default": "lightgray",
"description": "Color to use for null or masked values.",
"title": "Na Color",
"type": "string"
},
"na_in_legend": {
"default": true,
"description": "Whether to include null values in the legend.",
"title": "Na In Legend",
"type": "boolean"
},
"ncols": {
"default": 4,
"description": "Number of columns for multiple plots.",
"title": "Ncols",
"type": "integer"
},
"neighbors_key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Where to look for neighbors connectivities.",
"title": "Neighbors Key"
},
"outline_color": {
"default": [
"black",
"white"
],
"description": "Color of the outline for highlighted points.",
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "string"
},
{
"type": "string"
}
],
"title": "Outline Color",
"type": "array"
},
"outline_width": {
"default": [
0.3,
0.05
],
"description": "Width of the outline for highlighted points.",
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "number"
},
{
"type": "number"
}
],
"title": "Outline Width",
"type": "array"
},
"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"
},
"scale_factor": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Scale factor for the plot.",
"title": "Scale Factor"
},
"size": {
"anyOf": [
{
"type": "number"
},
{
"items": {
"type": "number"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Point size. If None, is automatically computed.",
"title": "Size"
},
"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"
},
"title": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Title for the plot.",
"title": "Title"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Use .raw attribute of adata for coloring with gene expression.",
"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"
},
"wspace": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Width space between panels.",
"title": "Wspace"
}
},
"required": [
"basis"
],
"title": "EmbeddingModel",
"type": "object"
}