pl_rank_genes_groups_dotplot
Visualize ranked differentially expressed genes (DEGs) using dot plots to analyze gene expression patterns across groups. Configure color maps, gene lists, and group comparisons for detailed insights in single-cell RNA sequencing studies.
Instructions
Plot ranking of genes(DEGs) using dotplot visualization. Defualt plot DEGs for rank_genes_groups tool
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. | |
| groups | No | The groups for which to show the gene ranking. | |
| key | No | Key used to store the ranking results in adata.uns. | |
| 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. | |
| min_logfoldchange | No | Value to filter genes in groups if their logfoldchange is less than the min_logfoldchange. | |
| n_genes | No | Number of genes to show. This can be a negative number to show down regulated genes. Ignored if var_names is passed. | |
| palette | No | Colors to use for plotting categorical annotation groups. | |
| use_raw | No | Use raw attribute of adata if present. | |
| values_to_plot | No | Instead of the mean gene value, plot the values computed by sc.rank_genes_groups. | |
| 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_names | No | Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes) to check their fold changes or p-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 rank_genes_groups_dotplot 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"
},
"groups": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "The groups for which to show the gene ranking.",
"title": "Groups"
},
"key": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Key used to store the ranking results in adata.uns.",
"title": "Key"
},
"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"
},
"min_logfoldchange": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "Value to filter genes in groups if their logfoldchange is less than the min_logfoldchange.",
"title": "Min Logfoldchange"
},
"n_genes": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Number of genes to show. This can be a negative number to show down regulated genes. Ignored if var_names is passed.",
"title": "N Genes"
},
"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"
},
"use_raw": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Use raw attribute of adata if present.",
"title": "Use Raw"
},
"values_to_plot": {
"anyOf": [
{
"enum": [
"scores",
"logfoldchanges",
"pvals",
"pvals_adj",
"log10_pvals",
"log10_pvals_adj"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Instead of the mean gene value, plot the values computed by sc.rank_genes_groups.",
"title": "Values To Plot"
},
"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_names": {
"anyOf": [
{
"items": {
"type": "string"
},
"type": "array"
},
{
"additionalProperties": {
"items": {
"type": "string"
},
"type": "array"
},
"type": "object"
}
],
"default": null,
"description": "Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes) to check their fold changes or p-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": "RankGenesGroupsDotplotModel",
"type": "object"
}