pyani.scripts.subcommands.subcmd_plot module

Provides the plot subcommand for pyani.

pyani.scripts.subcommands.subcmd_plot.subcmd_plot(args: argparse.Namespace) → int

Produce graphical output for an analysis.

Parameters:args – Namespace of command-line arguments

This is graphical output for representing the ANI analysis results, and takes the form of a heatmap, or heatmap with dendrogram.

pyani.scripts.subcommands.subcmd_plot.write_distribution(run_id: int, matdata: pyani.pyani_tools.MatrixData, outfmts: List[str], args: argparse.Namespace) → None

Write distribution plots for each matrix type.

Parameters:

• run_id – int, run_id for this run
• matdata – MatrixData object for this distribution plot
• args – Namespace for command-line arguments
• outfmts – list of output formats for files

pyani.scripts.subcommands.subcmd_plot.write_heatmap(run_id: int, matdata: pyani.pyani_tools.MatrixData, result_labels: Dict[KT, VT], result_classes: Dict[KT, VT], outfmts: List[str], args: argparse.Namespace) → None

Write a single heatmap for a pyani run.

Parameters:

• run_id – int, run_id for this run
• matdata – MatrixData object for this heatmap
• result_labels – dict of result labels
• result_classes – dict of result classes
• args – Namespace for command-line arguments
• outfmts – list of output formats for files

pyani.scripts.subcommands.subcmd_plot.write_run_plots(run_id: int, session, outfmts: List[str], args: argparse.Namespace) → None

Write all heatmaps for a specified run to file.

Parameters:

• run_id – int, run identifier in database session
• session – Session, active SQLite session
• outfmts – list of output format types
• args – Namespace, command line arguments

pyani.scripts.subcommands.subcmd_plot.write_scatter(run_id: int, matdata1: pyani.pyani_tools.MatrixData, matdata2: pyani.pyani_tools.MatrixData, result_labels: Dict[KT, VT], result_classes: Dict[KT, VT], outfmts: List[str], args: argparse.Namespace) → None

Write a single scatterplot for a pyani run.

Parameters:

• run_id – int, run_id for this run
• matdata1 – MatrixData object for this scatterplot
• matdata2 – MatrixData object for this scatterplot
• result_labels – dict of result labels
• result_classes – dict of result classes
• args – Namespace for command-line arguments
• outfmts – list of output formats for files