Metabolite Interaction Visualization

---
name: metabolite-interaction-visualization
description: Use when after computing a Jacobian matrix from covariance data in MInfer,
  when you need to render metabolite-to-metabolite interaction networks as publication-quality
  figures.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3083
  edam_topics:
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3172
  - http://edamontology.org/topic_0092
  tools:
  - R
  - MInfer
  - igraph
  - tidygraph
  license_tier: open
  provenance_tier: literature
derived_from:
- doi: 10.1016/j.cmpb.2025.108672
  title: MInfer
evidence_spans:
- MInfer is an R package
- MInfer is an R package designed for analyzing metabolomics data
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_minfer_cq
    doi: 10.1016/j.cmpb.2025.108672
    title: MInfer
  dedup_kept_from: coll_minfer_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1016/j.cmpb.2025.108672
  all_source_dois:
  - 10.1016/j.cmpb.2025.108672
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# metabolite-interaction-visualization

## Summary

Transform a computed Jacobian matrix into a network graph visualization where metabolites are nodes and interaction coefficients are directed, weighted edges. This skill bridges quantitative metabolomic analysis and interpretable network representations, enabling rapid identification of key metabolite dependencies and interaction directionality.

## When to use

After computing a Jacobian matrix from covariance data in MInfer, when you need to render metabolite-to-metabolite interaction networks as publication-quality figures. Use this skill when you have numerical Jacobian coefficients and want to communicate interaction strength and directionality visually rather than inspect raw matrix values.

## When NOT to use

- Input is a raw metabolomics abundance table or feature matrix — use covariance generation and Jacobian computation first.
- Jacobian matrix has not been computed or validated; spurious near-zero coefficients will clutter the network with false edges.
- No biological context or metabolite identifiers are available to label nodes meaningfully.

## Inputs

- Jacobian matrix (numerical matrix output from calculate_jacobian or equivalent)
- Metabolite identifiers (KEGG IDs or labels matching matrix row/column names)
- Optional: significance threshold or coefficient cutoff for edge filtering

## Outputs

- Network graph object (igraph or tidygraph representation)
- Network visualization (2D plot with positioned nodes and weighted edges)
- Publication-quality figure file (e.g., PNG, PDF with metabolite labels and edge encodings)

## How to apply

Load the computed Jacobian matrix into R. Extract edge information by identifying non-zero or statistically significant Jacobian coefficients that represent metabolite-to-metabolite interactions. Construct a directed network graph object using igraph or tidygraph, with metabolites as nodes and coefficients as edge weights. Apply a network layout algorithm (e.g., force-directed) to position nodes in 2D space for visual clarity. Encode interaction strength and direction using edge weights, colors, or line thickness. Render the final network with metabolite labels and save as a high-resolution figure suitable for publication.

## Related tools

- **MInfer** (R package providing Jacobian matrix computation and integrated visualization functions (visualize_heatmap, visualize_3d, network rendering)) — https://github.com/cellbiomaths/MInfer
- **igraph** (R graph library for constructing and laying out network objects from Jacobian coefficients)
- **tidygraph** (Alternative R graph library for network construction and manipulation using tidy data principles)
- **R** (Host language and environment for MInfer, igraph/tidygraph operations, and visualization rendering)

## Examples

```
visualize_heatmap(jacobian_6C$J, title="Jacobian Matrix - 6C")
```

## Evaluation signals

- Network graph has exactly N nodes (one per metabolite) with row and column names from Jacobian matrix correctly mapped.
- Edges are present only where Jacobian coefficients exceed the specified significance threshold; edge weights or colors scale monotonically with coefficient magnitude.
- Edge directionality (arrows, if applicable) reflects the sign and biological interpretation of interaction (e.g., positive/negative feedback).
- Node layout is reproducible and visually separable (no overlapping labels); layout algorithm converges without errors.
- Figure is saved in a standard publication format (PNG, PDF, SVG) at sufficient resolution (≥300 dpi) with visible metabolite labels and a legend or colorbar explaining edge encoding.

## Limitations

- Network readability degrades rapidly with >50–100 metabolites; consider filtering to a subset of high-confidence or high-magnitude interactions before visualization.
- Jacobian matrix computation assumes linear dynamics and may not capture non-linear or higher-order metabolite interactions.
- Layout algorithms are stochastic; reproducibility requires setting a random seed or using deterministic layout methods (e.g., hierarchical, circular).
- Edge weight encoding (color, thickness) is subjective; threshold selection for edge inclusion is not automated and must be justified by the analyst.

## Evidence

- [other] Extract edge information and construct network: "Extract edge information from the Jacobian matrix by identifying non-zero or significant coefficients that represent metabolite-to-metabolite interactions. Construct a network graph object"
- [other] Apply layout and render visualization: "Apply network layout algorithm to position nodes in 2D space for clarity. Render the network visualization with metabolite labels, edge weights or colors to encode interaction strength and direction,"
- [intro] MInfer integration and workflow: "MInfer includes visualization tools as part of its workflow for analyzing metabolomics data, following Jacobian matrix computation to render metabolite interaction networks."
- [readme] MInfer capabilities and purpose: "MInfer is an R package designed for analyzing metabolomics data. It provides tools for data preparation, covariance matrix generation, Jacobian matrix computation, and visualization of metabolite"
- [readme] Visualization functions available: "Visualize the Jacobian matrices using a heatmap or 3D plot: # Heatmap visualization visualize_heatmap(jacobian_6C$J, title = "Jacobian Matrix - 6C") # 3D visualization visualize_3d(jacobian_16C$J)"