Table 1 PhenoGram plotting options and arguments (− arg name) for creating PhenoGram plots using pheno_gram.rb

-h --help

Show the help message and exit

-v --version

Show PhenoGram version

-i input filename

Filename of input configuration file

-o output filename

Filename of output plot

-t title

Main plot title (enclose in double quotes)

-f image type

Output image format (default is PNG); other options depend on ImageMagick installation

-p phenotype spacing

Determines standard, equal, or alternative algorithm

-c color range

Determines random, web, generator, group, or list algorithm

-z --high-res

Sets plot resolution to 1200 DPI

-C --chrom-only

Plot only chromosomes with position

-S --small-circle

Plot with smaller phenotype circles

-O --outline-circle

Plot phenotype circles with black outline

-Z zoom location

Zoom on chromosome (i.e. 7) or region (i.e. 7:10000–20000)

-a --include-annotation

Include annotation on plot

-T --trans-lines

Show more transparent lines on chromosomes

-n --thin-lines

Show thinner lines across chromosomes

-B --thick-boundary

Increase thickness of chromosome boundary

-F --big-font

Increase font size of phenotype labels

-x –shade-chromatin

Add shading to inaccessible or cytogenetic chromosome regions

-r random seed

Seed for random number generator (default is 7)