mapper-fl

Mapper Landscapes

A topological map of fitness landscapes in maize

This repo contains the scripts and data necessary for reproducing the analyses performed in Manuscript.Name.

Citation

Rodriguez, J., M. Carrière, E. Millet, A. Desbiez-Piat, F. Chazal, and R.J. Wisser, MANUSCRIPT.TITLE. JOURNAL.NAME YEAR, XX, XX https://LINK.TO.DOI

Data:

• Data/
  • metadata/
    • admixture_subpop_groups_d.csv
  • raw_blues/
    • modeled_unadjusted_pheno_data_mapper_d.csv
  • data_phenotypes_adjusted.txt: Adjusted phenotypic data. Mean normalized across experiments using a subset of common genotypes across experiments.
  • data_phenotypes_adjusted_scaled.txt: Adjusted and center-scaled phenotypic data.
  • Flowering.1d.geno__phate_result.rds: 3D PHATE embedding of genotype matrix

Scripts:

• Scripts/

  • 01_combine_pheno_data.R: Combines phenotypic data from different experiments to obtain adjusted means.
  • 02_compare_alpha_shapes.R: Compares the alpha shapes between genetic groups for the ecophysiological traits.
  • 03_pheno_mapper_tune.R: Mapper landscape - ecophysiological feature space.
  • 04_geno_mapper_tune.R: Mapper landscape - genetic feature space.
  • 05_mapper_components.R: Post-processing Mapper landscapes
  • 06_gp_cumeffect.R: Genetic heterogeneity analysis

• [Helpers]

  • identify_igraph_loops.R: Auxiliary script to identify loops and cycles in mapper graphs.
  • mapper_instability.py: Auxiliary script to compute instability metrics for mapper graphs.
  • mapper_tune_main_d.py: Constructs mapper graphs for a range of graph parameterizations and returns instability metrics.
  • path_selection_occupancy.R: Trajectory selection via node occupancy
  • path_selection_cld.R: Trajectory selection via CLD

Figures: