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

From: Visualizing genomic information across chromosomes with PhenoGram

Usage: 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)