EJSAHN/sorghum-seed-spectral-manifold

Analysis pipeline for the Senegal sorghum seed spectral manifold and hyperspectral GWAS, including inter-seed distribution post-GWAS QTL mapping. # Sorghum Seed Spectral Manifold This repository contains the analysis workflow used for downstream spectral, morphology, GWAS, and inter-seed heterogeneity analyses in Senegalese sorghum seeds. ## Repository layout - `main/sorghum_spectral_main.py` - Core manuscript analysis pipeline - Builds spectral summary matrices from processed inputs - Merges morphology and spectral traits - Constructs genotype PCs - Prepares GEMMA inputs and summarizes GWAS/QTL results - Runs path analysis and in silico manifold perturbation - Annotates GWAS summaries with sorghum gene models - `main/sorghum_interseed_postgwas.py` - Post-GWAS processing for inter-seed optical heterogeneity traits - Summarizes QTLs from GEMMA association outputs - Maps intervals to candidate genes - Enriches descriptions with annotation resources - `support/support_tables.py` - Additional downstream summary analyses (tables only; no figure generation) - Computes empirical LD decay, genotype PCA scree, chromosome 6 local summaries, locus-level peak tables, and related summary outputs - `support/support_core.py` - Shared utilities for the downstream summary analyses ## What is not included - Figure-generation or figure-refinement scripts used only for manuscript layout - Exploratory or troubleshooting notebooks - Raw hyperspectral image cubes - Platform-specific executables (for example, PLINK or GEMMA binaries) ## Data sources expected by this repository Please see `docs/input_data_sources.md` for the full list. In brief: - Seed morphology phenotype data: previously published supplementary data - SNP genotype data: public Figshare repository - Curated spectral and GWAS summary tables: Supplementary Data S1 of the manuscript - Raw hyperspectral image data: available from the corresponding author upon reasonable request ## External tools This repository does not bundle GEMMA or PLINK. - The core manuscript script prepares GEMMA input files and summarizes outputs after external GEMMA execution. - Th …