The tutorial requires four input files. By default, the command-line script looks for:
input/example_pixy_fst_data.csv
input/example_pixy_pi_data.csv
input/example_comparison_map.txt
input/example_chromosome_map.txt
The Fst and π examples are comma-separated. The two map files are tab-separated. The command-line script also accepts tab-separated Fst and π files when their filenames do not end in .csv.
Required columns:
pop1 pop2 chromosome window_pos_1 window_pos_2 avg_wc_fst
Required columns:
pop chromosome window_pos_1 window_pos_2 avg_pi
Each row defines one pairwise comparison:
comp population_1 population_2 plot_order
Population names must exactly match the names in the pixy files. population_1 is the numerator and population_2 is the denominator of the π ratio. Comparison names must use the format population_1.v.population_2.
Each row connects a chromosome name in the pixy output to its numeric plot label and order:
chromosome chromo.num
Supply custom filenames after the project directory. Relative paths are resolved from the project directory:
Rscript scripts/meadow_plot_cli.R PROJECT_DIR FST_FILE PI_FILE COMPARISON_MAP_FILE CHROMOSOME_MAP_FILE [MAX_INTERVENING_NONOUTLIERS]For example:
Rscript scripts/meadow_plot_cli.R /path/to/project input/my_fst.tsv input/my_pi.tsv input/my_comparisons.txt input/my_chromosomes.txt 3