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cafferychen777

ChatSpatial

by cafferychen777
OverviewSchemaRelated ServersScoreDiscussions
Python
Hybrid

visualize_data

Destructive

Generate spatial transcriptomics visualizations by specifying plot type and parameters for gene expression, deconvolution, and cell communication.

Instructions

Visualize spatial transcriptomics data. Set plot_type and subtype in params; see VisualizationParameters schema for all options.

Args:
    data_id: Dataset ID
    params: Visualization parameters (plot_type, subtype, genes, output_format, dpi, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paramsNo
data_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed3 schema fields changedv1.5.3
    • addedInput schema / $defs / VisualizationParameters / properties / colormap / description
      Added value: +"Colormap for continuous values. Categorical features automatically use a qualitative palette; set a qualitative palette such as 'tab20' to override that selection."
    • changedInput schema / $defs / VisualizationParameters / properties / subplot_wspace / default
      Previous value: -0New value: +0.3
    • changedInput schema / $defs / VisualizationParameters / properties / subplot_wspace / description
      Previous value: -"Horizontal subplot spacing. Lower for tighter, higher for looser."New value: +"Horizontal subplot spacing as a fraction of axis width. The default leaves room for y-axis tick labels; lower it for tighter panels once axes are hidden."
  2. Changed8 schema fields changedv1.3.2
    • addedInput schema / $defs / VisualizationParameters / properties / alpha / maximum
      Added value: +1
    • addedInput schema / $defs / VisualizationParameters / properties / alpha / minimum
      Added value: +0
    • addedInput schema / $defs / VisualizationParameters / properties / dpi / exclusiveMinimum
      Added value: +0
    • changedInput schema / $defs / VisualizationParameters / properties / figure_size / anyOf
      Previous value: -[
-  {
-    "items": {
-      "type": "integer"
-    },
-    "maxItems": 2,
-    "minItems": 2,
-    "type": "array"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "items": {
+      "exclusiveMinimum": 0,
+      "type": "integer"
+    },
+    "maxItems": 2,
+    "minItems": 2,
+    "type": "array"
+  },
+  {
+    "type": "null"
+  }
+]
    • changedInput schema / $defs / VisualizationParameters / properties / panel_layout / anyOf
      Previous value: -[
-  {
-    "items": {
-      "type": "integer"
-    },
-    "maxItems": 2,
-    "minItems": 2,
-    "type": "array"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "items": {
+      "exclusiveMinimum": 0,
+      "type": "integer"
+    },
+    "maxItems": 2,
+    "minItems": 2,
+    "type": "array"
+  },
+  {
+    "type": "null"
+  }
+]
    • changedInput schema / $defs / VisualizationParameters / properties / spot_size / anyOf
      Previous value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]New value: +[
+  {
+    "exclusiveMinimum": 0,
+    "type": "number"
+  },
+  {
+    "type": "null"
+  }
+]
    • addedInput schema / additionalProperties
      Added value: +false
    • addedOutput schema / additionalProperties
      Added value: +false
  3. Changed1 schema field changedv1.2.8
    • changedInput schema / $defs / VisualizationParameters / properties / subtype / description
      Previous value: -"Visualization subtype. Options by plot_type:\n- expression: 'heatmap'|'violin'|'dotplot'|'correlation'\n- deconvolution: 'spatial_multi'|'pie'|'dominant'|'diversity'|'umap'|'imputation'\n- communication: 'dotplot'|'tileplot'|'circle_plot'\n- trajectory: 'pseudotime'|'circular'|'fate_map'|'gene_trends'|'fate_heatmap'|'palantir'\n- velocity: 'stream'|'phase'|'proportions'|'heatmap'|'paga'\n- statistics: 'neighborhood'|'co_occurrence'|'ripley'|'moran'|'centrality'|'getis_ord' (required)\n- enrichment: 'barplot'|'dotplot'\n- cnv: 'heatmap'|'spatial'\n- integration: 'batch'|'cluster'|'highlight'"New value: +"Visualization subtype. Options by plot_type:\n- expression: 'heatmap'|'violin'|'dotplot'|'correlation'\n- deconvolution: 'spatial_multi'|'pie'|'dominant'|'diversity'|'umap'|'imputation'\n- communication: 'spatial'|'dotplot'|'tileplot'|'circle_plot'\n- trajectory: 'pseudotime'|'circular'|'fate_map'|'gene_trends'|'fate_heatmap'|'palantir'\n- velocity: 'stream'|'phase'|'proportions'|'heatmap'|'paga'\n- statistics: 'neighborhood'|'co_occurrence'|'ripley'|'moran'|'centrality'|'getis_ord' (required)\n- enrichment: 'barplot'|'dotplot'\n- cnv: 'heatmap'|'spatial'\n- integration: 'batch'|'cluster'|'highlight'"
  4. First observedv1.2.7

TDQS

B3.2/5.0
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations flag destructiveHint=true and readOnlyHint=false, so this tool may have side effects, but the description only mentions visualization and parameters. It does not disclose overwriting behavior, file side effects, or any other consequences. This is not a direct contradiction, but the description misses important behavioral context.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is short and front-loaded with the purpose, followed by a pointer to the schema. The Args block is mostly redundant with the schema but remains concise and does not significantly bloat the description.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the very large VisualizationParameters schema, the pointer to that schema is helpful, and the output schema covers return values. However, the description lacks workflow context, side-effect awareness, and guidance on how visualization relates to upstream analysis steps. It is minimally viable but has clear gaps.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The schema itself is highly detailed with property descriptions, so the description does not need to duplicate that information. It usefully highlights plot_type and subtype as primary controls and points to the VisualizationParameters schema. However, the example 'genes' does not exactly match the schema property 'feature', adding slight ambiguity.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description begins with a specific verb and resource: 'Visualize spatial transcriptomics data.' This clearly distinguishes it from sibling tools like load_data, preprocess_data, and find_markers. The added instruction to set plot_type and subtype further scopes the tool's functionality.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description tells users to set plot_type and subtype and reference the schema, but it does not explain when to use this tool versus alternatives, prerequisites, or when not to use it. No exclusions or alternative tool references are provided.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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