Usage

This section describes how to use pyRona. All options as of version 0.3.3 are described here.

Parameters

  • Getting help

    • Simply calling the program, or issuing the single argument -h will print all the available options on the console

  • Positional arguments:

    • The first argument should be the name of the program whose results you wish to analyse. pyRona can take one of two options here:

      • baypass:Process Baypass results
      • lfmm:Process LFMM results

    • Depending on which you choose, some of the other options will be different.

  • I/O options

    • pyRona requires several files as input, that should be specified in the following options:
      • Common options to both Baypass and LFMM:
        • -pc: File containing current environmental variables, formatted as per the upstream program input (Baypass or LFMM)
        • -fc: File containing future environmental variables, formatted as per the upstream program input (Baypass or LFMM)
        • -out: File where the plot will be saved. This option is extension aware, and entering the extension as "PDF", "SVG" or "PNG", will make pyRona save the plot in the respective format
        • -map: File where a RONA map will be saved. This options is also extension aware. In order to draw the map, cartopy must be installed on your system (see Installation) -map assumes that the first variable in the environmental file is "Latitude" and the second one is "Longitude"
        • -covar_names: File containing the name of each environmental variable. Use it if you want your plots to be named accoring to the used variables, instead of numbered. Each line of this file should contain a variable name in the same order as in the covariates file
      • Baypass specific options:
        • -pop: File with names of populations (one population per line)
        • -beta: BayPass output "summary_betai"
        • -pij: BayPass output "PIJ"
      • LFMM specific options:
        • -assoc: File containing a matrix of p-values as outputted by LFMM
      • -geno: The input file used for LFMM. Should be in the LFMM format

  • Parameters

    • pyRona requires some parameters to be set in order to perform the analysis. These are:
      • Common options to both Baypass and LFMM:
        • -covars: [optional] Number of covars to calculate the RONA for (default: 3)
        • -remove-outliers: [optional] Pass this option if you want to pyRona to calculate the regression trend-line after removing any coordinates considered outliers
        • -immutables: Covariates to skip from the environmental variables file. Useful to skip variables that are the same in te present covars and future covars file, such as latitude (default: 1 2 3)
        • -ronatype: Defines the RONA is calculated. absdiff performs calculations as described in Rellstab et al. 2016 - using the absolute value of the differences, diff uses the differences without modulus, and dist accounts simply for the distance between the future condition and the trendline (default: absdiff)
      • Baypass specific options:
        • -bf: Bayes Factor threshold. This is the value above which associations are considered significant
      • LFMM specific options:
        • -P: p-value threshold. This is the value below which associations are considered significant

  • Other options (all optional)

    • pyRona allows for setting some further miscellaneous options:
      • draw-ind-plots: Passing this options with a path to a directory will cause pyRona to draw each individual "covar-marker" plot. If it is omitted, no individual plots are drawn.
      • -no-weighted-means: Set this option to "1" or "True" if you wish to use means instead of weighted means for the RONA calculation

Example runs:

pyRona baypass -pc Popfiles/ENVFILE -fc Popfiles/ENVFILE_rpc26 -beta Analyses/Baypass/mcmc_aux/Qsuber_GBS_07_loki_mcmc_aux_summary_betai.out -pij Analyses/Baypass/mcmc_aux/Qsuber_GBS_07_loki_mcmc_aux_summary_pij.out -pop Popfiles/popnames_single_GEO.txt -bf 15 -outliers 0 -out ~/Desktop/rpc26.pdf -covars 4

This command will execute pyRona set to analyse Baypass output using the input files specified by -pc, -fc, -beta, -pij and -pop, using the value 15 as the BF threshold, skipping outlier removal and calculating the RONA value for the most frequent 4 associated environmental variables. The plot will be saved as a PDF under ~/Desktop/rpc26.pdf.

pyRona lfmm -pc ~/aa/present_covars.txt -fc ~/aa/RCP26_covars.txt -out ~/Desktop/LFMM_rpc26.pdf -P 0.01 -assoc ~/aa/scaled_lfmm_results.csv -geno ~/aa/qsuber.lfmm

This command will execute pyRona set to analyse LFMM output using the input files specified by -pc, -fc, -assoc and -geno, using the value 0.01 as the p-value threshold, skipping outlier removal (default) and calculating the RONA value for the most frequent 3 associated environmental variables (default). The plot will be saved as a PDF under ~/Desktop/LFMM_rpc26.pdf.