mkt.databases.cli.plot_dict_kinase

CLI to plot the DICT_KINASE figures from YAML-configured aesthetics.

Renders the study-independent KinaseInfo figures built from the shipped DICT_KINASE archive: the source-coverage upset plot, the combined UniProt->KLIFS residue map with inter-/intra-region gap violins, and the KLIFS hierarchical conservation-tree supplement (static split figures + interactive Bokeh explorer). Each figure is rendered only when its config section is present in the YAML (the non-tree figures are rendered when no config is given).

Following mkt_impact.cli.run_analysis, the figures are registered in a _PLOT_STEPS dict keyed by config section, so adding a figure is one entry.

This CLI deliberately does not import mkt.databases.datasets.process (which has a network side effect on import); the conservation-tree renderers are imported lazily inside their steps so the panel build only runs when requested.

Functions

_plot_conservation_tree(dict_kinase, ...)	Static KLIFS conservation-tree supplement (summary + top/bottom panels).
_plot_conservation_tree_explorer(...)	Interactive KLIFS conservation-tree Bokeh explorer (standalone HTML).
_plot_region_gap_violin(dict_kinase, ...)	UniProt->KLIFS residue map with inter-/intra-region gap violins.
_plot_residue_dot(dict_kinase, output_dir, cfg)	Static per-amino-acid KLIFS dot-plot figure (default cysteine).
_plot_residue_dot_explorer(dict_kinase, ...)	Interactive per-amino-acid KLIFS dot-plot Bokeh explorer (standalone HTML).
_plot_upset(dict_kinase, output_dir, cfg)	Source-coverage upset plot over the DICT_KINASE archive.
_write_clade_membership_table(dict_kinase, ...)	LaTeX table of named conservation clades and their member kinases.
main([config_path, verbose])	Generate the DICT_KINASE figures.

mkt.databases.cli.plot_dict_kinase._plot_conservation_tree(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

Static KLIFS conservation-tree supplement (summary + top/bottom panels).

mkt.databases.cli.plot_dict_kinase._plot_conservation_tree_explorer(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

Interactive KLIFS conservation-tree Bokeh explorer (standalone HTML).

mkt.databases.cli.plot_dict_kinase._plot_region_gap_violin(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

UniProt->KLIFS residue map with inter-/intra-region gap violins.

mkt.databases.cli.plot_dict_kinase._plot_residue_dot(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

Static per-amino-acid KLIFS dot-plot figure (default cysteine).

mkt.databases.cli.plot_dict_kinase._plot_residue_dot_explorer(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

Interactive per-amino-acid KLIFS dot-plot Bokeh explorer (standalone HTML).

mkt.databases.cli.plot_dict_kinase._plot_upset(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

Source-coverage upset plot over the DICT_KINASE archive.

mkt.databases.cli.plot_dict_kinase._write_clade_membership_table(dict_kinase: dict, output_dir: str, cfg: DictKinaseFiguresConfig) → None

LaTeX table of named conservation clades and their member kinases.

mkt.databases.cli.plot_dict_kinase.main(config_path: ~pathlib.Path | None = <typer.models.OptionInfo object>, verbose: ~typing.Annotated[bool, <typer.models.OptionInfo object at 0x7754019d6920>] = False) → None

Generate the DICT_KINASE figures.

Loads aesthetics from a YAML config file when --config is provided, otherwise uses defaults. Each figure is rendered only when its config section (one of _PLOT_STEPS) is present in the YAML; with no config the always-cheap non-tree figures (_DEFAULT_SECTIONS) are rendered.