subcmd_plot.rst

pyani plot

The plot subcommand will plot the results of an ANI analysis, specified by run_id, contained within a local SQLite3 database, located at dbpath. Plot files will be written to the outdir directory.

usage: pyani plot [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
              [--citation] -o OUTDIR --run_ids RUN_ID [RUN_ID ...]
              [--dbpath DBPATH] [--formats FORMAT [FORMAT ...]]
              [--method METHOD] [--workers WORKERS]

Flagged arguments

--dbpath DBPATH

Path to the location of the local pyani database to be used. Default: .pyani/pyanidb

--disable_tqdm

Disable the tqdm progress bar while the plotting process runs. This is useful when testing to avoid aesthetic problems with test output.

--formats FORMAT [FORMAT ...]

Graphics output format(s); more than one can be specified. Valid options are: (pdf/png/svg/jpg). (default: png)

-l LOGFILE, --logfile LOGFILE

Provide the location LOGFILE to which a logfile of the plotting process will be written.

--method METHOD

Graphics method to use for plotting; options (seaborn, mpl, plotly). (default: seaborn)

-o OUTDIR, --o outdir OUTDIR

Path to a directory where comparison plot files will be written.

--run_ids RUN_ID [RUN_ID ...]

Unique database ID of the runs to be plotted.