% vtools_report plot_geno_fields -h
usage: vtools_report plot_geno_fields [-h] [--variants TABLE]
                                      [--samples [SAMPLES [SAMPLES ...]]]
                                      [--genotypes [GENOTYPES [GENOTYPES ...]]]
                                      [--save_data FILENAME]
                                      [--save_script FILENAME] [--width px]
                                      [--height px] [--hist name]
                                      [--norm_curve] [--dot name]
                                      [--dot_size pt]
                                      [--discrete_color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}]
                                      [--box name] [--stratify C [C ...]]
                                      [--outlier_size pt]
                                      [--color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}]
                                      [-v {0,1,2}]
                                      fields [fields ...]

positional arguments:
  fields                A list of genotype fields that will be outputted.

optional arguments:
  -h, --help            show this help message and exit
  --variants TABLE      Limit value of fields to variant in specified variant
                        table. Default to all variants.
  --samples [SAMPLES [SAMPLES ...]]
                        Conditions based on which samples are selected.
                        Default to all samples.
  --genotypes [GENOTYPES [GENOTYPES ...]]
                        Conditions based on which genotypes are selected.
                        Default to all variants.
  --save_data FILENAME  Save data to file.
  --save_script FILENAME
                        Save R script to file.
  --width px            Width of plot. Default to 800.
  --height px           Height of plot. Default to 600.
  -v {0,1,2}, --verbosity {0,1,2}
                        Output error and warning (0), info (1) and debug (2)
                        information of vtools and vtools_report. Debug
                        information are always recorded in project and
                        vtools_report log files.

Draw histogram:
  --hist name           File name of the outputted figure, which can have type
                        PDF, EPS, or JPG. Multiple files might be produced if
                        more than one figure is produced (e.g.
                        MyFig_$FIELD1.pdf, MyFig_$FILED2.pdf if MyFig.pdf is
  --norm_curve          Add a normal distribution N(mean, stdev) density curve
                        to the histogram.

Draw dot plot. Allow up to 3 input fields: for single input
    field, the values will be plotted on y-axis with index being x-axis; for two input fields, the first
    field will be plotted on x-axis and the second field on y-axis; for three input fields, values of
    the third input field is represented by color of the dots.:
  --dot name            File name of the outputted figure, which can have type
                        PDF, EPS, or JPG.
  --dot_size pt         Size of dots. Default is 2.0
  --discrete_color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}
                        If specified, the third field of input will be treated
                        as "factor" data.

Draw box plot. Allow one or more input fields and produce
    box plot for all fields in one graph. With --stratify option, box plot will be generated for field
    in different strata, if there is only one input field, or for the first field in different strata of
    the second field, if there are two input fields.:
  --box name            File name of the outputted figure, which can have type
                        PDF, EPS, or JPG.
  --stratify C [C ...]  Cutoff values to stratify data in the input field for
                        box plot. When this option is on, only one input field
                        is allowed.
  --outlier_size pt     Size of outlier dots. Default is 2.0
  --color {Dark2,grayscale,default,BrBG,PiYG,PRGn,PuOr,RdBu,RdGy,RdYlBu,RdYlGn,Spectral,Accent,Paired,Pastel1,Pastel2,Set1,Set2,Set3,Blues,BuGn,BuPu,GnBu,Greens,Greys,Oranges,OrRd,PuBu,PuBuGn,PuRd,Purples,RdPu,Reds,YlGn,YlGnBu,YlOrBr,YlOrRd}
                        Color theme for boxes.


Histograms, dot plots and box plots can be generated for variant info fields. The command interface is similar to vtools_report plot_pheno_fields.