Subcommand: cathedral plot

Synopsis: Create a cathedral plot, using the pre-computated cathedral data.

Usage: grenedalf cathedral-plot [options]

Documentation for grenedalf v0.3.0

Options

Input

--json-path

TEXT:PATH(existing)=[] ... Excludes: --csv-path
List of json files or directories to process. For directories, only files with the extension .json are processed. To input more than one file or directory, either separate them with spaces, or provide this option multiple times.

--csv-path

TEXT:PATH(existing)=[] ... Excludes: --json-path
List of csv files or directories to process. For directories, only files with the extension .csv are processed. To input more than one file or directory, either separate them with spaces, or provide this option multiple times.

Color

--color-list

TEXT=inferno
List of colors to use for the palette. Can either be the name of a color list, a file containing one color per line, or an actual comma-separated list of colors. Colors can be specified in the format #rrggbb using hex values, or by web color names.

--reverse-color-list

FLAG
If set, the order of colors of the --color-list is reversed.

--under-color

TEXT=#ff00ff
Color used to indicate values below the min value. Color can be specified in the format #rrggbb using hex values, or by web color names.

--clip-under

FLAG
Clip (i.e., clamp) values less than min to be inside [ min, max ], by setting values that are too low to the specified min value. If set, --under-color is not used to indicate values out of range.

--over-color

TEXT=#00ffff
Color used to indicate values above the max value. Color can be specified in the format #rrggbb using hex values, or by web color names.

--clip-over

FLAG
Clip (i.e., clamp) values greater than max to be inside [ min, max ], by setting values that are too high to the specified max value. If set, --over-color is not used to indicate values out of range.

--clip

FLAG
Clip (i.e., clamp) values to be inside [ min, max ], by setting values outside of that interval to the nearest boundary of it. This option is a shortcut to set --clip-under and --clip-over at once.

--color-normalization

TEXT:{linear,logarithmic}=linear
To create the cathedral plot, the value of each pixel needs to be translated into a color, by mapping from the range of values into the range of the color map. This translation can be done as a simple linear transform, or logarithmic, so that low values can be distinguished with more detail.

--min-value

FLOAT=nan
As an alternative to determining the range of values automatically, the range limits can be set explicitly. This allows for instance to cap the visualization in cases of outliers that would otherwise hide detail in the lower values. Any value that is below the min specified here will then be mapped to the under color, or clipped to the lowest value in the color map.

--max-value

FLOAT=nan
See --min-value; this is the equivalent upper limit of values.Any value that is above the max specified here will then be mapped to the over color, or be clipped to the highest value in the color map.

Output

--out-dir

TEXT=.
Directory to write files to

--file-prefix

TEXT
File prefix for output files. Most grenedalf commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.

--file-suffix

TEXT
File suffix for output files. Most grenedalf commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.

Global Options

--allow-file-overwriting

FLAG
Allow to overwrite existing output files instead of aborting the command.

--verbose

FLAG
Produce more verbose output.

--threads

UINT
Number of threads to use for calculations. If not set, we guess a reasonable number of threads, by looking at the environmental variables (1) OMP_NUM_THREADS (OpenMP) and (2) SLURM_CPUS_PER_TASK (slurm), as well as (3) the hardware concurrency, taking hyperthreads into account, in the given order of precedence.

--log-file

TEXT
Write all output to a log file, in addition to standard output to the terminal.

Citation

When using this method, please do not forget to cite

Lucas Czech, Jeffrey Spence, Moises Exposito-Alonso. grenedalf: population genetic statistics for the next generation of pool sequencing. arXiv, 2023. doi:10.48550/arXiv.2306.11622