# Command line interface¶

The command line interface (CLI) ist the common way to use Gecos. It offers a range of options to customize the way color schemes are generated.

## Color space¶

The color space, in which the color scheme is optimized can be limited. The range of L*a*b* values, as well as the minimum and maximum saturation can be set. The saturation $$s$$ is the euclidean distance from gray at the same lightness:

$s = \sqrt{{a^*}^2 + {b^*}^2}$

The following table shows which CLI option to use in order to set the lower or upper limit of a color space value.

Lower limit

Upper limit

L*

--lmin

--lmax

a*

--amin

--amax

b*

--bmin

--bmax

s

--smin

--smax

If you would like to display only the customized color space and skip the color scheme generation use the --dry-run/-n option.

## Substitution matrix and alphabet¶

An alphabet is defined as the set of symbols a sequence may contain. For example the unambiguous nucleobase alphabet contains the four symbols A, C, G and T.

By default Gecos creates a color scheme for the amino acid alphabet based on the BLOSUM62 substitution matrix.

To change the substitution matrix, either a valid NCBI substitution matrix name (e.g. PAM250) or a path to a text file containing a substitution matrix in NCBI format can be given to the --matrix/-m option.

To create a color scheme for another alphabet (e.g. nucleobases or a structural alphabet), the --alphabet/-a option needs to be set. The option takes a string, where each character is treated as individual symbol (e.g. "ACGT" for nucleobases). Therefore, multi-character symbols are not allowed. For multi-character symbols refer to the Python API instead.

## Optimization¶

Based on the color space, the substitution matrix and the alphabet, the optimizer tries to find a color scheme that optimally matches the matrix. In order to increase the quality of the scheme tha amount of optimization steps (--nsteps) or the number of runs (--nruns) can be increased. However, increasing these values also extends the runtime of the optimization. Note that --nruns can take advantage of multiple cores. The number of used cores is set with --nthreads

The simulated annealing can be adjusted even more fine grained by setting the inverse temperature at the first (--beta-start) and last (--beta-end) step of the optimization. For the steps in between the inverse temperature is interpolated exponentially. The step size decreases in the course of the simulated annealing also in an exponential manner, which can be parameterized via --stepsize-start and --stepsize-end. The seed for the random number generator used by the algorithm is set with the --seed option. However, these parameters address the more advanced users.

A color can be fixed for a certain symbol by giving a (symbol, L*, a*, b*) tuple to the --constraint/-c option (e.g. A 50 0 0). The option can be repeated to fix the color for multiple symbols. In addition to the relative color difference the optimizer also tries to find a scheme with a high contrast. The weighting of the importance of the contrast is adjusted with --contrast.

The formula used for calculation of perceptual color differences ($$\Delta E$$) can be set via the --delta option. While the default formula 'CIEDE2000' yields the most accurate results, 'CIE76' features the fastest calculation.

## Output files¶

If no output files are specified, Gecos simply outputs the generated color scheme in JSON format to STDOUT. Alternatively, the scheme can be directly saved to a file specified via --scheme-file/-f. The name of the scheme inside the file is set with --name. Optionally, the score values throughout the simulation can be saved via --score-file for further analysis.

## Visualization¶

Gecos provides some visualization tools for direct evaluation of a color space or a generated color scheme:

 --show-space Shows the color space, including the user-supplied limitations. --show-scheme Shows conformation of symbols in the selected color space. --show-score Shows the score values throughout the simulation. --show-example Shows an example multiple protein sequence alignment using the new color scheme. Cannot be combined with a custom alphabet.

--show-space and --show-scheme show a 2D a*b* cross section of the 3D color space. The L* value of this section is set with --lightness/-l.