runchuan-bu/bioclaw/bio-figure-design

bio-figure-design

Step 6: Figure design (Figure 详细设计)

Design the manuscript figures panel by panel, including the figure logic, panel content, and caption intent.

Purpose

1. Design Figure 1 as the method / framework overview
2. Design Figures 2-N as task-driven application figures
3. Plan supplementary figures
4. Draft figure captions
5. Keep figure logic synchronized with manuscript claims

Input Format

topic: [research topic]
task_system: [task system]
dataset_catalog: [dataset catalog]
metric_system: [metric system]
analysis_system: [analysis system]
target_journal: [optional, default nat-communications]

Workflow

Step 6.1: Design Figure 1

Figure 1 should explain the overall method and paper framing:

• Panel a: method / model overview
• Panel b: data or modality overview
• Panel c: task overview
• Panel d: metric overview
• Panel e: analysis overview

The goal is to make the full manuscript logic visible in one figure.

Step 6.2: Design Figures 2-N

Each application figure should be task-first:

• one major task per figure
• panel a: data flow / experimental setup
• panels b-d: quantitative evaluation
• panel e or later: qualitative / biological validation

This keeps the paper organized around claims rather than around plots.

Step 6.3: Supplementary figures

Use supplementary figures for:

• ablations
• robustness checks
• extra markers
• extended datasets
• alternative parameter settings

Step 6.4: Caption planning

Every figure should have a caption plan that explains:

• what each panel shows
• what claim it supports
• what dataset it uses
• what metric or biological conclusion it demonstrates

Output Format

# Figure Designs
 
## Figure 1: Framework Overview
-Panel a:
-Panel b:
-Panel c:
-Panel d:
-Panel e:
-Caption intent:
 
## Figure 2: [Task 1]
-Panel a:
-Panel b:
-Panel c:
-Panel d:
-Panel e:
-Caption intent:
 
## Figure 3: [Task 2]
...
 
## Supplementary Figures
-Supplementary Figure 1:
-Supplementary Figure 2:
 
## Design Notes
-visual consistency
-panel ordering logic
-expected take-home message per figure
 
## Next Step
-Use the figure plan to draft manuscript text in Step 7

Figure Design Principles

1. One main claim per figure
2. Quantitative evidence should appear before broad interpretation
3. Biological validation should be visible, not hidden
4. Reviewer-facing clarity matters more than decorative complexity
5. Figure order should match the manuscript story

Usage

/bio-figure-design "topic: spatial multi-omics integration | task_system: [...] | dataset_catalog: [...] | metric_system: [...] | analysis_system: [...] | target_journal: nat-communications"

Notes

1. Keep Figure 1 conceptual and clean.
2. For application figures, tie every panel to a concrete task and metric.
3. Do not overload a figure if a supplementary figure can carry the extra material.