Upset Plot Converter

Upset Plot Converter

Convert complex Venn diagrams (more than 4 sets) to clearer Upset Plots.

When to Use

Key Features

Dependencies

See ## Prerequisites above for related details.

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Data Analytics/upset-plot-converter"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan: 1. Confirm the user input, output path, and any required config values. 2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings. 3. Run python scripts/main.py with the validated inputs. 4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

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

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work. 2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions. 3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available. 4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items. 5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Usage

from skills.upset_plot_converter.scripts.main import convert_venn_to_upset
From set data
sets = {
    'A': {1, 2, 3, 4, 5},
    'B': {4, 5, 6, 7, 8},
    'C': {3, 5, 7, 9, 10},
    'D': {2, 4, 6, 8, 10},
    'E': {1, 3, 5, 7, 9}
}
convert_venn_to_upset(sets, output_path="upset_plot.png")
From list data
from skills.upset_plot_converter.scripts.main import upset_from_lists
set_names = ['Genes A', 'Genes B', 'Genes C', 'Genes D', 'Genes E']
lists = [
    ['gene1', 'gene2', 'gene3'],
    ['gene2', 'gene4', 'gene5'],
    ['gene3', 'gene5', 'gene6'],
    ['gene7', 'gene8', 'gene9'],
    ['gene1', 'gene10', 'gene11']
]
upset_from_lists(set_names, lists, output_path="gene_upset.png", title="Gene Intersections")

Input

Output

PNG file of the Upset Plot visualization.

Notes

Requirements

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

Lifecycle Status

Output Requirements

Every final response should make these items explicit when they are relevant:

Error Handling

Input Validation

This skill accepts requests that match the documented purpose of upset-plot-converter 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:

> upset-plot-converter 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:

1. Objective 2. Inputs Received 3. Assumptions 4. Workflow 5. Deliverable 6. Risks and Limits 7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.

from skills.upset_plot_converter.scripts.main import convert_venn_to_upset
From set data
sets = {
    'A': {1, 2, 3, 4, 5},
    'B': {4, 5, 6, 7, 8},
    'C': {3, 5, 7, 9, 10},
    'D': {2, 4, 6, 8, 10},
    'E': {1, 3, 5, 7, 9}
}
convert_venn_to_upset(sets, output_path="upset_plot.png")
From list data
from skills.upset_plot_converter.scripts.main import upset_from_lists
set_names = ['Genes A', 'Genes B', 'Genes C', 'Genes D', 'Genes E']
lists = [
    ['gene1', 'gene2', 'gene3'],
    ['gene2', 'gene4', 'gene5'],
    ['gene3', 'gene5', 'gene6'],
    ['gene7', 'gene8', 'gene9'],
    ['gene1', 'gene10', 'gene11']
]
upset_from_lists(set_names, lists, output_path="gene_upset.png", title="Gene Intersections")

Python dependencies
pip install -r requirements.txt