pedview

A lightweight command-line tool for visualizing family pedigrees in genetics and clinical research workflows.

pedview reads standard pedigree files and generates self-contained, interactive HTML reports with publication-ready SVG diagrams. It has zero external runtime dependencies (built purely on Python standard library) and runs completely offline.

Features

• Zero Runtime Dependencies: Pure Python standard library (math, html, dataclasses, pathlib, argparse).
• Flexible Input: Auto-detects standard 6-column PLINK .fam/.ped files and extended headered pedigree files.
• Clinical & Research Attributes: Visualizes affected status, proband indicators, carriers, deceased status, age labels, and genotype calls.
• Layered Graph Engine: Sugiyama-style layout with barycenter crossing reduction, twin handling, and consanguinity loop routing.
• Interactive Standalone HTML: Produces a single offline HTML report with pan/zoom navigation, individual detail drawer, and search.
• Publication Exports: One-click download for vector SVG, journal-styled SVG, and high-resolution PNG.
• Mendelian Quality Control: Automated parent-child relationship validation and Wright's inbreeding coefficient calculations ($f_a$).

Installation

pip install pedview

Or install from source:

git clone https://github.com/DKunLee/Pedview.git
cd Pedview
pip install .

Quickstart

# 1. Validate pedigree format, integrity, and relationships
pedview validate <input.ped>

# 2. Preview family and cohort summaries directly in the terminal
pedview preview <input.ped>

# 3. Build a standalone interactive HTML report
pedview build <input.ped> -o <output_report.html>

# 4. Render a single family from a multi-family cohort
pedview build <input.ped> --family <family_id> -o <family_report.html>

# 5. Highlight a candidate variant and set ancestor inbreeding coefficient
pedview build <input.ped> --variant-name "<variant_name>" --ancestor-inbreeding 0.02 -o <output_report.html>

Supported Formats

1. Standard Headerless PLINK .fam / .ped (6 Columns)

FAM01 101 0   0   1 1
FAM01 102 0   0   2 1
FAM01 201 101 102 1 2
FAM01 202 101 102 2 1

• Sex: 1 = Male, 2 = Female, 0 = Unknown.
• Phenotype: 1 = Unaffected, 2 = Affected, 0 / -9 = Unknown.
• Missing Parents: 0, ., -9, NA.

2. Headered Extended Pedigree (Tab- or Space-delimited)

famid  id   fid  mid  sex  affected    proband  deceased  age  genotype
FAM01  101  0    0    1    unaffected  0        1         72y  0/0
FAM01  102  0    0    2    unaffected  0        0         68y  0/1
FAM01  201  101  102  1    affected    1        0         14y  0/1

Common column header aliases are resolved automatically:

• Family: famid, family_id, family, pedigree, fid
• Individual: id, iid, individual_id, sample_id
• Father: fid, pat, pid, father, father_id
• Mother: mid, mat, mother, mother_id
• Sex: sex, gender
• Phenotype: affected, phenotype, affection

CLI Reference

Build Options

• -o, --output: Output file path (defaults to <input>.html).
• --family: Filter report to a specific family ID (<family_id>).
• --title: Custom title for the HTML report ("<title>").
• --variant-name: Candidate variant annotation label (e.g. "<variant_name>").
• --ancestor-inbreeding: Global Wright ancestor inbreeding coefficient ($f_a$). Defaults to 0.0.

License

This project is licensed under the MIT License.