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forest-plot-styler Analyze data with `forest-plot-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
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Zip 다운로드 다운로드 중... eval_report_forest-plot-styler_result.json 10.4 KB name forest-plot-styler description Analyze data with `forest-plot-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation. license MIT author AIPOCH
Source : https://github.com/aipoch/medical-research-skills
Forest Plot Styler
ID: 157
Beautifies Meta-analysis or subgroup analysis forest plots, customizes Odds Ratio point sizes and confidence interval line styles.
When to Use
Use this skill when the task needs Beautify meta-analysis forest plots with customizable odds ratio points.
Use this skill for data analysis tasks that require explicit assumptions, bounded scope, and a reproducible output format.
Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.
Key Features
See ## Features above for related details.
Scope-focused workflow aligned to: Analyze data with forest-plot-styler using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
Packaged executable path(s): scripts/main.py.
Reference material available in references/ for task-specific guidance.
Structured execution path designed to keep outputs consistent and reviewable.
Dependencies
Python >= 3.8
matplotlib >= 3.5.0
pandas >= 1.3.0
numpy >= 1.20.0
openpyxl >= 3.0.0 (for reading Excel)
Example Usage See ## Usage above for related details.
cd "20260318/scientific-skills/Data Analytics/forest-plot-styler"
python -m py_compile scripts/main.py
python scripts/main.py --help
Confirm the user input, output path, and any required config values.
Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
Run python scripts/main.py with the validated inputs.
Review the generated output and return the final artifact with any assumptions called out.
Implementation Details See ## Workflow above for related details.
Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
Primary implementation surface: scripts/main.py.
Reference guidance: references/ contains supporting rules, prompts, or checklists.
Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.
Quick Check Use this command to verify that the packaged script entry point can be parsed before deeper execution.
python -m py_compile scripts/main.py
Audit-Ready Commands Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.
python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py --input "Audit validation sample with explicit symptoms, history, assessment, and next-step plan." --format json
Workflow
Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.
Features
Reads Meta-analysis data (CSV/Excel format)
Draws high-quality forest plots
Customizes Odds Ratio point sizes, colors, and shapes
Customizes confidence interval line styles (color, thickness, endpoint style)
Supports subgroup analysis display
Automatically calculates and displays pooled effect values
Outputs to PNG, PDF, or SVG format
Usage python -m py_compile scripts/main.py
# Example invocation: python scripts/main.py --input <data.csv> [options]
Parameters Parameter Type Default Required Description --input, -istring - Yes Input data file (CSV or Excel) --output, -ostring forest_plot.png No Output file path --format, -fstring png No Output format (png/pdf/svg) --point-sizeint 8 No OR point size --point-colorstring #2E86AB No OR point color --ci-colorstring #2E86AB No Confidence interval line color --ci-linewidthint 2 No Confidence interval line thickness --ci-capwidthint 5 No Confidence interval endpoint width --summary-colorstring #A23B72 No Pooled effect point color --summary-shapestring diamond No Pooled effect point shape --subgroupstring - No Subgroup analysis column name --title, -tstring Forest Plot No Chart title --xlabel, -xstring Odds Ratio (95% CI) No X-axis label --reference-linefloat 1.0 No Reference line position --width, -Wint 12 No Image width (inches) --height, -Hint auto No Image height (inches) --dpiint 300 No Image resolution --font-sizeint 10 No Font size --style, -sstring default No Preset style (default/minimal/dark)
Input Data Format CSV/Excel files must contain the following columns:
Column Name Description Type studyStudy name Text orOdds Ratio value Numeric ci_lowerConfidence interval lower bound Numeric ci_upperConfidence interval upper bound Numeric weightWeight (optional, for point size) Numeric subgroupSubgroup label (optional) Text
Sample Data study,or,ci_lower,ci_upper,weight,subgroup
Study A,0.85,0.65,1.12,15.2,Drug A
Study B,0.72,0.55,0.94,18.5,Drug A
Study C,1.15,0.88,1.50,12.3,Drug B
Study D,0.95,0.75,1.20,14.8,Drug B
Examples
Basic Usage python scripts/main.py -i meta_data.csv
Custom Style python scripts/main.py -i meta_data.csv \
--point-color="#E63946" \
--ci-color="#457B9D" \
--point-size=10 \
--ci-linewidth=3 \
-t "Meta-Analysis of Treatment Effects"
Subgroup Analysis python scripts/main.py -i meta_data.csv \
--subgroup subgroup_column \
--summary-color="#F4A261" \
-o subgroup_forest.png
Output PDF Vector Graphic python scripts/main.py -i meta_data.csv \
-f pdf \
-o forest_plot.pdf
Preset Styles
default
Blue color scheme
Standard font size
White background
minimal
Clean lines
Grayscale color scheme
No grid lines
dark
Dark background
Bright data points
Suitable for dark theme presentations
Output Example Generated forest plot contains:
Left side: Study name list
Middle: OR values and confidence intervals
Right side: Weight percentage (if available)
Bottom: Pooled effect value (diamond marker)
Reference line (OR=1)
Notes
Ensure input file encoding is UTF-8
OR values are automatically converted when log scale is suggested
Studies with confidence intervals crossing 1 are not statistically significant
Weight values are used to adjust point size, reflecting study contribution
Risk Assessment Risk Indicator Assessment Level Code Execution Python/R scripts executed locally Medium Network Access No external API calls Low File System Access Read input files, write output files Medium Instruction Tampering Standard prompt guidelines Low Data Exposure Output files saved to workspace Low
Security Checklist
Prerequisites
# Python dependencies
pip install -r requirements.txt
Evaluation Criteria
Success Metrics
Test Cases
Basic Functionality : Standard input → Expected output
Edge Case : Invalid input → Graceful error handling
Performance : Large dataset → Acceptable processing time
Lifecycle Status
Current Stage : Draft
Next Review Date : 2026-03-06
Known Issues : None
Planned Improvements :
Performance optimization
Additional feature support
Output Requirements Every final response should make these items explicit when they are relevant:
Objective or requested deliverable
Inputs used and assumptions introduced
Workflow or decision path
Core result, recommendation, or artifact
Constraints, risks, caveats, or validation needs
Unresolved items and next-step checks
Error Handling
If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
Do not fabricate files, citations, data, search results, or execution outcomes.
Input Validation This skill accepts requests that match the documented purpose of forest-plot-styler and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
forest-plot-styler only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Response Template Use the following fixed structure for non-trivial requests:
Objective
Inputs Received
Assumptions
Workflow
Deliverable
Risks and Limits
Next Checks
If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.
Inputs to Collect
Required inputs: the user goal, the primary data or source file, and the requested output format.
Optional inputs: output directory, formatting preferences, and validation constraints.
If a required input is unavailable, return a short clarification request before continuing.
Output Contract
Return a short summary, the main deliverables, and any assumptions that materially affect interpretation.
If execution is partial, label what succeeded, what failed, and the next safe recovery step.
Keep the final answer within the documented scope of the skill.
Validation and Safety Rules
Validate identifiers, file paths, and user-provided parameters before execution.
Do not fabricate results, metrics, citations, or downstream conclusions.
Use safe fallback behavior when dependencies, credentials, or required inputs are missing.
Surface any execution failure with a concise diagnosis and recovery path.