python easy_psmc_plot.py --help
Usage: easy_psmc_plot.py [OPTIONS]
Options:
--psmc_file_list TEXT a list with all samples name and line color,
seperate by (This parameter are required!)
--bin_size INTEGER Bin size used to generate the imput of PSMC
(default: 100)
--mutation_rate FLOAT Mutation rate per generation(Default: 4.78e-9)
--generation_time INTEGER Number of year per generation(Default: 20)
--x_min FLOAT Size of the plot xlim lower(Default: 1e4)
--x_max FLOAT Size of the plot xlim upper(Default: 1e8)
--y_min FLOAT Size of the plot ylim lower(Default: 0)
--y_max FLOAT Size of the plot ylim upper(Default: 30e4)
--line_width FLOAT The line width(Default: 2.0)
--length FLOAT Length of the plot(Default:10)
--height FLOAT Height of the plot(Default:5)
--picture_dpi INTEGER Output picture dpi(Default:300)
--span_min FLOAT the span of xlim selection region's min
value(Default:None)
--span_max FLOAT the span of xlim selection region's max
value(Default:None)
--span_color TEXT the span color(Default:purple)
--span_alpha FLOAT the span clolor transparency(Default:0.3)
--help Show this message and exit.
python easy_psmc_plot.py --psmc_file_list sample_list.txt --mutation_rate 7.8e-9 --generation_time 6 --x_max 7e4 --y_max 0.5e4 --x_min 1e3 --span_min 1.5e3 --span_max 1.9e3 --span_color yellow