Command-line arguments

DESCRIPTION:
  vcfstats v0.2.0: Powerful VCF statistics.

USAGE:
  vcfstats --vcf PATH --outdir AUTO --formula LIST --title LIST [OPTIONS]

REQUIRED OPTIONS:
  -v, --vcf <PATH>          - The VCF file.
  -o, --outdir <AUTO>       - The output directory.
  -f, --formula <LIST>      - The formulas for plotting in format of Y ~ X,
                              where Y and X should be either an entry or an
                              aggregation.
  --title <LIST>            - The title of each figure, will be used to name the
                              output files as well.

OPTIONAL OPTIONS:
  --loglevel <STR>          - The logging level. Default: info
  --figtype <LIST>          - Your preferences for type of plot for each
                              formula. Default: \[]
  --figfmt <LIST>           - Your preferences for format of figure for each
                              formula, Any file format supported by matplotlib.
                              Default is png. Default: \[]
  -r, --region <LIST>       - Regions in format of CHR or CHR:START-END
                              Default: \[]
  -R, --Region <AUTO>       - Regions in a BED file. If both --region/--Region
                              are provided, regions will be merged together.
                              Default: None
  -p, --passed [BOOL]       - Only analyze variants that pass all filters.
                              This does not work if FILTER entry is in the
                              analysis.
                              Default: False
  -l, --list [BOOL]         - List all available macros. Default: False
  -s, --savedata [BOOL]     - Whether save the plotting data for further
                              exploration. Default: False
  --macro <PATH>            - A user-defined macro file. Default: None
  --ggs <LIST>              - Extra ggplot2 expressions for each plot
                              Default: \[]
  --devpars <NS>            - The device parameters for plots. To specify
                              devpars for each plot, use a configuration file.
  -c, --config <AUTO>       - A configuration file defining how to plot in TOML
                              format.
                              If this is provided, CLI arguments will be
                              overwritten if defined in this file. Default: None
  -h, --help                - Print help information for this command

OPTIONAL OPTIONS UNDER --devpars:
  --devpars.width <INT>     - The width of the plot Default: 2000
  --devpars.height <INT>    - The height of the plot Default: 2000
  --devpars.res <INT>       - The resolution of the plot Default: 300

You can specify regions using -r/--region and/or -R/--Region, however, you have to make sure regions are not overlapping, otherwise, variants in the overlapping regions will be redundant in the calculations.
To define you macros, you'd better use docstr, so that you can use -l/--list to check out your macros

You can generate multiple plots in one run. Just specify multiple formulas and multiple titles. For example:

vcfstats --vcf examples/sample.vcf \
	--outdir vcfstats-out \
	--formula 'DEPTHs{0} ~ CHROM' 'AAF ~ CHROM' \
	--title 'Depth distribution on each chromosome' 'Allele frequency distribution on each chromosome'

You can also specify different figure types for different plots. If you want to keep ones as default, you can pass an empty string. For example:

vcfstats --vcf examples/sample.vcf \
	--outdir vcfstats-out \
	--formula 'DEPTHs{0} ~ CHROM' 'AAF ~ CHROM' \
	--title 'Depth distribution on each chromosome' 'Allele frequency distribution on each chromosome' \
	--figtype '' boxplot # using boxplot instead of violin for 2nd plot

Similar as --figtype, you can also use --ggs to modify the plots generated by ggplot2. Please refer to ggplot2 documentation.
However, for --devpars, you can only specify a universal parameters. To change each sub-parameter of it, you can do --devpars.res 70
To specify different devpars for different plots, you have to use a configuration file. Please refer to seciont Configuration file
To specify --ggs for multiple plots, you can do --ggs "theme_minimal()" "theme_dark()". If you have multiple ggs for the same plot, you need ; to seaprate them: --ggs "theme_minimal(); ylab('Count')" "theme_dark(); xlab('ABC')"