Sorghum Trait Analysis Pipeline

This project processes and visualizes sorghum root trait data using a Dockerized pipeline. It supports:

• Combining and cleaning raw Excel data
• Scaling and outlier correction
• Plotting trait comparisons (bar, line, heritability, etc.)
• Exporting plots as interactive HTML or static PNG (via Kaleido)

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Quick Start

1. Build the Docker Image

./pipeline.sh

2. Run a Plot Script

./pipeline.sh plot_heritability.py

All paths should use the** /srv/data/... form inside the container. This mounts your local **./data/ directory.

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Inputs

Place your input files in the data/ directory before running the pipeline:

• data/raw/ ↳ Directory of raw trait files *.xlsx. These will be combined and cleaned.
• data/meta.xlsx ↳ Metadata file mapping plot_number to Genotype and Condition.
• data/cleaned.xlsx ↳ Generated by the cleaning step; used as input for all plotting scripts.

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