pl_heatmap
Visualize gene expression patterns with customizable heatmaps for single-cell RNA sequencing data. Configure figure size, color scales, annotations, and group comparisons.
Instructions
Heatmap of the expression values of genes.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| color_map | No | Color map to use for continuous variables. | |
| dendrogram | No | If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added. | |
| figsize | No | Figure size. Format is (width, height). | |
| gene_symbols | No | Column name in .var DataFrame that stores gene symbols. | |
| groupby | Yes | The key of the observation grouping to consider. | |
| 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 |
| log | No | Plot on logarithmic axis. | |
| num_categories | No | Only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided. | |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| show_gene_labels | No | By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed. | |
| standard_scale | No | Whether or not to standardize that dimension between 0 and 1. | |
| swap_axes | No | By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names. | |
| use_raw | No | Use raw attribute of adata if present. | |
| var_group_labels | No | Labels for each of the var_group_positions that want to be highlighted. | |
| var_group_positions | No | Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions. | |
| var_group_rotation | No | Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees. | |
| var_names | No | var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values. | |
| 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. |
Input Schema (JSON Schema)
{
"description": "Input schema for the heatmap plotting tool.",
"properties": {
"color_map": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Color map to use for continuous variables.",
"title": "Color Map"
},
"dendrogram": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "string"
}
],
"default": false,
"description": "If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added.",
"title": "Dendrogram"
},
"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"
},
"gene_symbols": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Column name in .var DataFrame that stores gene symbols.",
"title": "Gene Symbols"
},
"groupby": {
"anyOf": [
{
"type": "string"
},
{
"items": {
"type": "string"
},
"type": "array"
}
],
"description": "The key of the observation grouping to consider.",
"title": "Groupby"
},
"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"
},
"log": {
"default": false,
"description": "Plot on logarithmic axis.",
"title": "Log",
"type": "boolean"
},
"num_categories": {
"default": 7,
"description": "Only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided.",
"exclusiveMinimum": 0,
"title": "Num Categories",
"type": "integer"
},
"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"
},
"show_gene_labels": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed.",
"title": "Show Gene Labels"
},
"standard_scale": {
"anyOf": [
{
"enum": [
"var",
"obs"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether or not to standardize that dimension between 0 and 1.",
"title": "Standard Scale"
},
"swap_axes": {
"default": false,
"description": "By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names.",
"title": "Swap Axes",
"type": "boolean"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Use raw attribute of adata if present.",
"title": "Use Raw"
},
"var_group_labels": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Labels for each of the var_group_positions that want to be highlighted.",
"title": "Var Group Labels"
},
"var_group_positions": {
"anyOf": [
{
"items": {
"maxItems": 2,
"minItems": 2,
"prefixItems": [
{
"type": "integer"
},
{
"type": "integer"
}
],
"type": "array"
},
"type": "array"
},
{
"type": "null"
}
],
"default": null,
"description": "Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions.",
"title": "Var Group Positions"
},
"var_group_rotation": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees.",
"title": "Var Group Rotation"
},
"var_names": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
}
],
"default": null,
"description": "var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values.",
"title": "Var Names"
},
"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"
}
},
"required": [
"groupby"
],
"title": "HeatmapModel",
"type": "object"
}