mishaploid / carrot-image-analysis

Scripts to process data and map QTL from carrot image analysis

Carrot Image Analysis

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

Phenotypic variation, correlations, and repeatability

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

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)