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visualize_data

Visualize spatial transcriptomics data with customizable plots for expression, deconvolution, cell communication, and more. Choose plot type and subtype, then adjust parameters to tailor the output.

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
data_idYes
paramsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

Annotations already indicate non-readOnly and openWorld behavior. The description does not elaborate on side effects (e.g., file saving via output_path) or other behavioral traits, adding minimal context beyond what annotations provide.

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, with a clear first sentence and an 'Args' section. It is concise and front-loaded, though the 'Args' list adds little beyond the schema.

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 complex schema and many sibling tools, the description provides domain context ('spatial transcriptomics') and directs to the schema. However, it lacks information about the return value (output schema exists but is not referenced) and does not explain how to interpret results.

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 description mentions 'plot_type and subtype' but not the many other parameters. The schema provides detailed descriptions for most nested properties, but the top-level params array has 0% schema coverage. The description partially compensates by directing users to the schema.

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 clearly states 'Visualize spatial transcriptomics data,' which is a specific verb-resource combination. This distinguishes it from sibling tools that are analytical (e.g., analyze_cell_communication, compute_embeddings) rather than visualization-focused.

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?

No explicit guidance on when to use this tool versus alternatives (e.g., after analysis steps). The purpose is implied, but there is no mention of prerequisites or exclusion criteria.

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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