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oh231 authored Jul 31, 2024
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This GitHub repository provides a comprehensive resource for analyzing high-throughput phenotyping (HTP) data from the [Ag Alumni Seed Phenotyping Facility (AAPF, Purdue)](https://ag.purdue.edu/aapf/), including a detailed guide and a collection of data processing tools. It includes foundational [R](https://www.r-project.org/) tools for transforming AAPF data products (RGB, hyperspectral, X-ray) into an analysis-ready dataset ([long format table](http://www.cookbook-r.com/Manipulating_data/Converting_data_between_wide_and_long_format/)). This standardized dataset can be directly used in statistical modeling and visualization using R.


## AAPF Data Guide
## AAPF Data Guide 📖

* [RGB imaging data (above-ground)](DataGuide_AAPF_RGB.md)
* [Hyperspectral imaging (HSI) data (above-ground)](DataGuide_AAPF_HSI.md)
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* Reshape data product (masterfile, .xlsx) into analysis-ready format
- [RGB and HSI data](reshape_rgb_hsi.r)
- [X-ray data](reshape_xray.r)
* Plant trait assessment
* Plant trait assessment 📐
- [Repeatability](calculate_repeatability.r)
* Visualization
* Visualization 😎
- [Overall comparison of repeatability from various sensors and camera positions](display.repeatability.r)
- [Variance of plant traits across hybrid, treatment, etc.](display_variance.r)
- [2D projections of high-dimensional clusters](display_cluster.r)
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