These scripts are for processing data from a carrot image analysis pipeline (available on CyVerse in the PhytoMorph Image Analysis Toolkit). For more detail, see Turner et al. (2018) An automated image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.) doi: 10.3389/fpls.2018.01703
01_combine_hand_measurements.R - cleans up raw phenotypic data and combines data from a diallel cross and an F2 mapping population
02_shootPCA.R - reads in results for the shoot biomass profile (SBP, generated through CyVerse) and performs principal component analysis
03_rootPCA.R - reads in results for the root biomass profile (generated through CyVerse) and performs principal component analysis on raw data and after normalization for length and width
04_merge_hand_image.R - combines hand and image derived measurements into a single file
05_correlations.R - plots correlations between hand and image-measured traits
06_repeatability.R - calculates repeatability within and across environments for all traits
qtl_mapping/create_input_file.R - creates input file for R/qtl using a linkage map and phenotype file
qtl_mapping/mqm_mapping.R - runs multiple qtl mapping (MQM) for all traits
qtl_mapping/permutations.R - dummy script for running permutations (see osg_scripts)
qtl_mapping/plot_qtl_results.R - generate LOD plots for all traits
osg_scripts/ - contains files and libraries necessary to run qtl mapping and permutation testing on the Open Science Grid (OSG)