mkt.databases.plot_config

Configuration dataclasses for plot_dataset_data.py.

Loads plot aesthetics and data source paths from YAML config files via OmegaConf, following the pattern used in mkt_impact.

Classes

`CladeMembershipTableConfig`([str_group, filename])	Params for the LaTeX clade-membership table.
`ColKinaseColorConfig`(construct_unaligned, ...)	RGB colors for sequence-type categories.
`ConservationTreeConfig`(min_cluster_size, ...)	Aesthetics for the static KLIFS conservation-tree supplemental figures.
`ConservationTreeExplorerConfig`([...])	Params for the interactive KLIFS conservation-tree Bokeh explorer.
`DataSourceConfig`([davis_csv, pkis2_csv, ...])	Paths to input data files (relative to repo root).
`DictKinaseFiguresConfig`(matplotlib_rc, ...)	Top-level config for the DICT_KINASE figures (upset + region-gap map/violin).
`DynamicRangePlotConfig`(figsize, font_size, ...)	Aesthetics for the dynamic-range histogram.
`FamilyColorConfig`([use_kinase_group_colors, ...])	Color palette for kinase families.
`MatplotlibRCConfig`([svg_fonttype, ...])	Global matplotlib rcParams applied before any plot.
`MetricsBoxplotConfig`(figsize, box_widths, ...)	Aesthetics for the metrics boxplot.
`OutputConfig`([subdir, bool_svg, bool_png, ...])	Output directory settings.
`PlotDatasetConfig`(matplotlib_rc, ...)	Top-level config aggregating all sub-configs.
`RegionGapViolinConfig`(figsize, ...)	Aesthetics for the combined UniProt->KLIFS map + region-gap violin figure.
`ResidueDotConfig`(amino_acid, ...)	Aesthetics for the static per-amino-acid KLIFS dot-plot figure.
`ResidueDotExplorerConfig`([min_cluster_size, ...])	Params for the interactive per-amino-acid KLIFS dot-plot Bokeh explorer.
`RidgelinePlotConfig`(figsize, overlap, scale, ...)	Aesthetics for the ridgeline plot.
`SequenceSchematicConfig`(figsize, ...)	Aesthetics for the sequence input schematic.
`StackedBarchartConfig`([...])	Aesthetics for the stacked bar chart.
`UpsetPlotConfig`(figsize, dict_colors, ...)	Aesthetics for the KinaseInfo source-coverage upset plot.
`VennDiagramConfig`(figsize, circle_alpha, ...)	Aesthetics for the Venn diagram.

class mkt.databases.plot_config.CladeMembershipTableConfig(str_group: str = 'TK', filename: str = 'clade_membership_table')[source]

Bases: object

Params for the LaTeX clade-membership table.

Rendered by mkt.databases.plot.write_clade_membership_table(): the named conservation clades within str_group and their member kinases.

__init__(str_group: str = 'TK', filename: str = 'clade_membership_table') → None

filename: str = 'clade_membership_table'

str_group: str = 'TK'

class mkt.databases.plot_config.ColKinaseColorConfig(construct_unaligned: list[float] = <factory>, klifs_region_aligned: list[float] = <factory>, klifs_residues_only: list[float] = <factory>)[source]

Bases: object

RGB colors for sequence-type categories.

__init__(construct_unaligned: list[float] = <factory>, klifs_region_aligned: list[float] = <factory>, klifs_residues_only: list[float] = <factory>) → None

as_rgb_dict() → dict[str, tuple[float, float, float]][source]: Return colors as 0-1 scaled RGB tuples keyed by category name.

construct_unaligned: list[float]

klifs_region_aligned: list[float]

klifs_residues_only: list[float]

class mkt.databases.plot_config.ConservationTreeConfig(min_cluster_size: int = 12, font_size: float = 4.0, split_index: int | None = 47, formats: list[str] = <factory>)[source]

Bases: object

Aesthetics for the static KLIFS conservation-tree supplemental figures.

Rendered by mkt.databases.conservation.KLIFSConservationTreeFigure (summary dendrogram + top/bottom detail panels).

__init__(min_cluster_size: int = 12, font_size: float = 4.0, split_index: int | None = 47, formats: list[str] = <factory>) → None

font_size: float = 4.0

formats: list[str]

min_cluster_size: int = 12

split_index: int | None = 47

class mkt.databases.plot_config.ConservationTreeExplorerConfig(min_cluster_size: int = 12, logo_cutoff: float = 0.1, name_trunc: int = 14, filename: str | None = None)[source]

Bases: object

Params for the interactive KLIFS conservation-tree Bokeh explorer.

Rendered by mkt.databases.conservation.KLIFSTreeConservationApp.

__init__(min_cluster_size: int = 12, logo_cutoff: float = 0.1, name_trunc: int = 14, filename: str | None = None) → None

filename: str | None = None

logo_cutoff: float = 0.1

min_cluster_size: int = 12

name_trunc: int = 14

class mkt.databases.plot_config.DataSourceConfig(davis_csv: str = 'data/davis_data_processed.csv', pkis2_csv: str = 'data/pkis2_data_processed.csv', metrics_csv: str = 'data/2025_val_stable_metrics.csv')[source]

Bases: object

Paths to input data files (relative to repo root).

__init__(davis_csv: str = 'data/davis_data_processed.csv', pkis2_csv: str = 'data/pkis2_data_processed.csv', metrics_csv: str = 'data/2025_val_stable_metrics.csv') → None

davis_csv: str = 'data/davis_data_processed.csv'

metrics_csv: str = 'data/2025_val_stable_metrics.csv'

pkis2_csv: str = 'data/pkis2_data_processed.csv'

class mkt.databases.plot_config.DictKinaseFiguresConfig(matplotlib_rc: ~mkt.databases.plot_config.MatplotlibRCConfig = <factory>, upset_plot: ~mkt.databases.plot_config.UpsetPlotConfig = <factory>, region_gap_violin: ~mkt.databases.plot_config.RegionGapViolinConfig = <factory>, conservation_tree: ~mkt.databases.plot_config.ConservationTreeConfig = <factory>, conservation_tree_explorer: ~mkt.databases.plot_config.ConservationTreeExplorerConfig = <factory>, residue_dot: ~mkt.databases.plot_config.ResidueDotConfig = <factory>, residue_dot_explorer: ~mkt.databases.plot_config.ResidueDotExplorerConfig = <factory>, clade_membership_table: ~mkt.databases.plot_config.CladeMembershipTableConfig = <factory>, output: ~mkt.databases.plot_config.OutputConfig = <factory>)[source]

Bases: object

Top-level config for the DICT_KINASE figures (upset + region-gap map/violin).

Consumed by the plot_dict_kinase CLI. Kept separate from PlotDatasetConfig so rendering these figures never imports the dataset-processing module (which has a network side effect on import).

__init__(matplotlib_rc: ~mkt.databases.plot_config.MatplotlibRCConfig = <factory>, upset_plot: ~mkt.databases.plot_config.UpsetPlotConfig = <factory>, region_gap_violin: ~mkt.databases.plot_config.RegionGapViolinConfig = <factory>, conservation_tree: ~mkt.databases.plot_config.ConservationTreeConfig = <factory>, conservation_tree_explorer: ~mkt.databases.plot_config.ConservationTreeExplorerConfig = <factory>, residue_dot: ~mkt.databases.plot_config.ResidueDotConfig = <factory>, residue_dot_explorer: ~mkt.databases.plot_config.ResidueDotExplorerConfig = <factory>, clade_membership_table: ~mkt.databases.plot_config.CladeMembershipTableConfig = <factory>, output: ~mkt.databases.plot_config.OutputConfig = <factory>) → None

clade_membership_table: CladeMembershipTableConfig

conservation_tree: ConservationTreeConfig

conservation_tree_explorer: ConservationTreeExplorerConfig

classmethod from_yaml(config_path: str | Path) → DictKinaseFiguresConfig[source]

Load a DictKinaseFiguresConfig from a YAML file.

Parameters:

config_pathstr | Path: Path to the YAML configuration file.

Returns:

DictKinaseFiguresConfig: Fully populated config instance.

matplotlib_rc: MatplotlibRCConfig

output: OutputConfig

region_gap_violin: RegionGapViolinConfig

residue_dot: ResidueDotConfig

residue_dot_explorer: ResidueDotExplorerConfig

upset_plot: UpsetPlotConfig

class mkt.databases.plot_config.DynamicRangePlotConfig(figsize: list[float] = <factory>, font_size: int = 14, axes_titlesize: int = 16, axes_labelsize: int = 14, figure_titlesize: int = 20, alpha: float = 0.25, bins: int = 100, color_pkis2: str = 'blue', color_davis: str = 'green', axvline_x: float = 99, axvline_color: str = 'red', title_fontsize: int = 20, title_fontweight: str = 'bold', title_y: float = 1.25, subtitle_fontsize: int = 16, subtitle_alpha: float = 0.75, subtitle_y: float = 1.16, axis_label_fontsize: int = 16, tick_labelsize: int = 14, filename: str = 'dynamic_range_histogram')[source]

Bases: object

Aesthetics for the dynamic-range histogram.

__init__(figsize: list[float] = <factory>, font_size: int = 14, axes_titlesize: int = 16, axes_labelsize: int = 14, figure_titlesize: int = 20, alpha: float = 0.25, bins: int = 100, color_pkis2: str = 'blue', color_davis: str = 'green', axvline_x: float = 99, axvline_color: str = 'red', title_fontsize: int = 20, title_fontweight: str = 'bold', title_y: float = 1.25, subtitle_fontsize: int = 16, subtitle_alpha: float = 0.75, subtitle_y: float = 1.16, axis_label_fontsize: int = 16, tick_labelsize: int = 14, filename: str = 'dynamic_range_histogram') → None

alpha: float = 0.25

axes_labelsize: int = 14

axes_titlesize: int = 16

axis_label_fontsize: int = 16

axvline_color: str = 'red'

axvline_x: float = 99

bins: int = 100

color_davis: str = 'green'

color_pkis2: str = 'blue'

figsize: list[float]

figure_titlesize: int = 20

filename: str = 'dynamic_range_histogram'

font_size: int = 14

subtitle_alpha: float = 0.75

subtitle_fontsize: int = 16

subtitle_y: float = 1.16

tick_labelsize: int = 14

title_fontsize: int = 20

title_fontweight: str = 'bold'

title_y: float = 1.25

class mkt.databases.plot_config.FamilyColorConfig(use_kinase_group_colors: bool = True, palette_name: str = 'tab10', palette_n_colors: int = 10, other_color: str = '#808080', families: list[str] | None = None)[source]

Bases: object

Color palette for kinase families.

Two modes:

use_kinase_group_colors=True (default): uses DICT_KINASE_GROUP_COLORS from mkt.schema.constants — a curated, colorblind-friendly mapping.
use_kinase_group_colors=False: builds colors from a seaborn palette (palette_name / palette_n_colors) with other_color for “Other”.

In both modes, families controls which families appear and their order. When families is None, the keys of DICT_KINASE_GROUP_COLORS are used.

__init__(use_kinase_group_colors: bool = True, palette_name: str = 'tab10', palette_n_colors: int = 10, other_color: str = '#808080', families: list[str] | None = None) → None

families: list[str] | None = None

get_colors() → dict[source]

Return a dict mapping family name to color.

Returns:

dict: Mapping of family names to color values.

other_color: str = '#808080'

palette_n_colors: int = 10

palette_name: str = 'tab10'

use_kinase_group_colors: bool = True

class mkt.databases.plot_config.MatplotlibRCConfig(svg_fonttype: str = 'path', pdf_fonttype: int = 42, text_usetex: bool = False)[source]

Bases: object

Global matplotlib rcParams applied before any plot.

__init__(svg_fonttype: str = 'path', pdf_fonttype: int = 42, text_usetex: bool = False) → None

pdf_fonttype: int = 42

svg_fonttype: str = 'path'

text_usetex: bool = False

class mkt.databases.plot_config.MetricsBoxplotConfig(figsize: list[float] = <factory>, box_widths: float = 0.6, box_alpha: float = 0.7, median_color: str = 'black', median_linewidth: int = 2, whisker_color: str = 'black', whisker_linewidth: float = 1.5, cap_color: str = 'black', cap_linewidth: float = 1.5, jitter_std: float = 0.04, jitter_alpha: float = 0.6, jitter_size: int = 50, jitter_color: str = 'black', xtick_fontsize: int = 14, ylabel_fontsize: int = 20, ylabel_text: str = 'MSE (Z-Score)', title_fontsize: int = 22, title_fontweight: str = 'bold', ytick_fontsize: int = 18, grid_alpha: float = 0.3, bracket_start_pct: float = 0.08, bracket_spacing_pct: float = 0.15, bracket_height_pct: float = 0.02, bracket_linewidth: float = 1.5, pvalue_fontsize: int = 14, pvalue_fontweight: str = 'bold', title_color_davis: str = 'black', title_color_pkis2: str = 'black', filename: str = 'metrics_boxplot')[source]

Bases: object

Aesthetics for the metrics boxplot.

__init__(figsize: list[float] = <factory>, box_widths: float = 0.6, box_alpha: float = 0.7, median_color: str = 'black', median_linewidth: int = 2, whisker_color: str = 'black', whisker_linewidth: float = 1.5, cap_color: str = 'black', cap_linewidth: float = 1.5, jitter_std: float = 0.04, jitter_alpha: float = 0.6, jitter_size: int = 50, jitter_color: str = 'black', xtick_fontsize: int = 14, ylabel_fontsize: int = 20, ylabel_text: str = 'MSE (Z-Score)', title_fontsize: int = 22, title_fontweight: str = 'bold', ytick_fontsize: int = 18, grid_alpha: float = 0.3, bracket_start_pct: float = 0.08, bracket_spacing_pct: float = 0.15, bracket_height_pct: float = 0.02, bracket_linewidth: float = 1.5, pvalue_fontsize: int = 14, pvalue_fontweight: str = 'bold', title_color_davis: str = 'black', title_color_pkis2: str = 'black', filename: str = 'metrics_boxplot') → None

box_alpha: float = 0.7

box_widths: float = 0.6

bracket_height_pct: float = 0.02

bracket_linewidth: float = 1.5

bracket_spacing_pct: float = 0.15

bracket_start_pct: float = 0.08

cap_color: str = 'black'

cap_linewidth: float = 1.5

figsize: list[float]

filename: str = 'metrics_boxplot'

grid_alpha: float = 0.3

jitter_alpha: float = 0.6

jitter_color: str = 'black'

jitter_size: int = 50

jitter_std: float = 0.04

median_color: str = 'black'

median_linewidth: int = 2

pvalue_fontsize: int = 14

pvalue_fontweight: str = 'bold'

title_color_davis: str = 'black'

title_color_pkis2: str = 'black'

title_fontsize: int = 22

title_fontweight: str = 'bold'

whisker_color: str = 'black'

whisker_linewidth: float = 1.5

xtick_fontsize: int = 14

ylabel_fontsize: int = 20

ylabel_text: str = 'MSE (Z-Score)'

ytick_fontsize: int = 18

class mkt.databases.plot_config.OutputConfig(subdir: str = 'images', bool_svg: bool = True, bool_png: bool = True, bool_pdf: bool = False)[source]

Bases: object

Output directory settings.

__init__(subdir: str = 'images', bool_svg: bool = True, bool_png: bool = True, bool_pdf: bool = False) → None

bool_pdf: bool = False

bool_png: bool = True

bool_svg: bool = True

subdir: str = 'images'

class mkt.databases.plot_config.PlotDatasetConfig(matplotlib_rc: ~mkt.databases.plot_config.MatplotlibRCConfig = <factory>, family_colors: ~mkt.databases.plot_config.FamilyColorConfig = <factory>, col_kinase_colors: ~mkt.databases.plot_config.ColKinaseColorConfig = <factory>, dynamic_range: ~mkt.databases.plot_config.DynamicRangePlotConfig = <factory>, ridgeline: ~mkt.databases.plot_config.RidgelinePlotConfig = <factory>, stacked_barchart: ~mkt.databases.plot_config.StackedBarchartConfig = <factory>, venn_diagram: ~mkt.databases.plot_config.VennDiagramConfig = <factory>, metrics_boxplot: ~mkt.databases.plot_config.MetricsBoxplotConfig = <factory>, sequence_schematic: ~mkt.databases.plot_config.SequenceSchematicConfig = <factory>, data_sources: ~mkt.databases.plot_config.DataSourceConfig = <factory>, output: ~mkt.databases.plot_config.OutputConfig = <factory>)[source]

Bases: object

Top-level config aggregating all sub-configs.

__init__(matplotlib_rc: ~mkt.databases.plot_config.MatplotlibRCConfig = <factory>, family_colors: ~mkt.databases.plot_config.FamilyColorConfig = <factory>, col_kinase_colors: ~mkt.databases.plot_config.ColKinaseColorConfig = <factory>, dynamic_range: ~mkt.databases.plot_config.DynamicRangePlotConfig = <factory>, ridgeline: ~mkt.databases.plot_config.RidgelinePlotConfig = <factory>, stacked_barchart: ~mkt.databases.plot_config.StackedBarchartConfig = <factory>, venn_diagram: ~mkt.databases.plot_config.VennDiagramConfig = <factory>, metrics_boxplot: ~mkt.databases.plot_config.MetricsBoxplotConfig = <factory>, sequence_schematic: ~mkt.databases.plot_config.SequenceSchematicConfig = <factory>, data_sources: ~mkt.databases.plot_config.DataSourceConfig = <factory>, output: ~mkt.databases.plot_config.OutputConfig = <factory>) → None

col_kinase_colors: ColKinaseColorConfig

data_sources: DataSourceConfig

dynamic_range: DynamicRangePlotConfig

family_colors: FamilyColorConfig

classmethod from_yaml(config_path: str | Path) → PlotDatasetConfig[source]

Load a PlotDatasetConfig from a YAML file.

Parameters:

config_pathstr | Path: Path to the YAML configuration file.

Returns:

PlotDatasetConfig: Fully populated config instance.

matplotlib_rc: MatplotlibRCConfig

metrics_boxplot: MetricsBoxplotConfig

output: OutputConfig

ridgeline: RidgelinePlotConfig

sequence_schematic: SequenceSchematicConfig

stacked_barchart: StackedBarchartConfig

venn_diagram: VennDiagramConfig

class mkt.databases.plot_config.RegionGapViolinConfig(figsize: list[float] = <factory>, height_ratios: list[float] = <factory>, width_ratios: list[float] = <factory>, hspace: float = 0.12, wspace: float = 0.06, left_adjust: float = 0.05, right_adjust: float = 0.985, top_adjust: float = 0.97, bottom_adjust: float = 0.085, use_ribbon: bool = False, inter_color: str = '#cfcfcf', intra_color: str = '#8c8c8c', ribbon_alpha: float = 0.3, map_name_fontsize: int = 21, map_range_fontsize: int = 17, map_track_fontsize: int = 25, map_region_fontsize: int = 12, map_ellipsis_fontsize: int = 32, map_legend_fontsize: int = 17, violin_fontsize: int = 22, fill_alpha: float = 0.3, violin_width: float = 0.85, violin_linewidth: float = 1.0, violin_edgecolor: str = '#333333', jitter_size: float = 7.0, jitter_std: float = 0.06, jitter_alpha: float = 0.8, jitter_edgecolor: str = 'black', jitter_linewidth: float = 0.25, jitter_mixed_color: str = 'orange', grid_alpha: float = 0.3, text_color: str = '#333333', ylabel_text: str = 'Number of residues', filename: str = 'region_gap_violin')[source]

Bases: object

Aesthetics for the combined UniProt->KLIFS map + region-gap violin figure.

The figure stacks the UniProt-to-KLIFS residue map (top, spanning the full width) over two grouped violin panels (inter- and intra-region gaps) on separate log-scaled axes. All statistics are computed on the fly.

__init__(figsize: list[float] = <factory>, height_ratios: list[float] = <factory>, width_ratios: list[float] = <factory>, hspace: float = 0.12, wspace: float = 0.06, left_adjust: float = 0.05, right_adjust: float = 0.985, top_adjust: float = 0.97, bottom_adjust: float = 0.085, use_ribbon: bool = False, inter_color: str = '#cfcfcf', intra_color: str = '#8c8c8c', ribbon_alpha: float = 0.3, map_name_fontsize: int = 21, map_range_fontsize: int = 17, map_track_fontsize: int = 25, map_region_fontsize: int = 12, map_ellipsis_fontsize: int = 32, map_legend_fontsize: int = 17, violin_fontsize: int = 22, fill_alpha: float = 0.3, violin_width: float = 0.85, violin_linewidth: float = 1.0, violin_edgecolor: str = '#333333', jitter_size: float = 7.0, jitter_std: float = 0.06, jitter_alpha: float = 0.8, jitter_edgecolor: str = 'black', jitter_linewidth: float = 0.25, jitter_mixed_color: str = 'orange', grid_alpha: float = 0.3, text_color: str = '#333333', ylabel_text: str = 'Number of residues', filename: str = 'region_gap_violin') → None

bottom_adjust: float = 0.085

figsize: list[float]

filename: str = 'region_gap_violin'

fill_alpha: float = 0.3

grid_alpha: float = 0.3

height_ratios: list[float]

hspace: float = 0.12

inter_color: str = '#cfcfcf'

intra_color: str = '#8c8c8c'

jitter_alpha: float = 0.8

jitter_edgecolor: str = 'black'

jitter_linewidth: float = 0.25

jitter_mixed_color: str = 'orange'

jitter_size: float = 7.0

jitter_std: float = 0.06

left_adjust: float = 0.05

map_ellipsis_fontsize: int = 32

map_legend_fontsize: int = 17

map_name_fontsize: int = 21

map_range_fontsize: int = 17

map_region_fontsize: int = 12

map_track_fontsize: int = 25

classmethod preprint_2026() → RegionGapViolinConfig[source]: Preset used by the 2026 preprint figures (current defaults).

ribbon_alpha: float = 0.3

right_adjust: float = 0.985

text_color: str = '#333333'

top_adjust: float = 0.97

use_ribbon: bool = False

violin_edgecolor: str = '#333333'

violin_fontsize: int = 22

violin_linewidth: float = 1.0

violin_width: float = 0.85

width_ratios: list[float]

wspace: float = 0.06

ylabel_text: str = 'Number of residues'

class mkt.databases.plot_config.ResidueDotConfig(amino_acid: str = 'C', min_cluster_size: int = 12, highlight_targets: bool = False, formats: list[str] = <factory>)[source]

Bases: object

Aesthetics for the static per-amino-acid KLIFS dot-plot figure.

Rendered by mkt.databases.conservation.KLIFSConservationTreeFigure.plot_residue_dot().

__init__(amino_acid: str = 'C', min_cluster_size: int = 12, highlight_targets: bool = False, formats: list[str] = <factory>) → None

amino_acid: str = 'C'

formats: list[str]

highlight_targets: bool = False

min_cluster_size: int = 12

class mkt.databases.plot_config.ResidueDotExplorerConfig(min_cluster_size: int = 12, default_aa: str = 'C', filename: str | None = None)[source]

Bases: object

Params for the interactive per-amino-acid KLIFS dot-plot Bokeh explorer.

Rendered by mkt.databases.conservation.KLIFSResidueDotApp.

__init__(min_cluster_size: int = 12, default_aa: str = 'C', filename: str | None = None) → None

default_aa: str = 'C'

filename: str | None = None

min_cluster_size: int = 12

class mkt.databases.plot_config.RidgelinePlotConfig(figsize: list[float] = <factory>, overlap: float = 0.1, scale: float = 1.5, fill_alpha: float = 0.5, edgecolor: str = 'black', edge_linewidth: float = 1.5, baseline_linewidth: float = 0.5, baseline_alpha: float = 0.3, ytick_fontsize: int = 20, title_fontsize: int = 22, title_fontweight: str = 'bold', title_color_davis: str = 'black', title_color_pkis2: str = 'black', xtick_fontsize: int = 18, xlabel_fontsize: int = 20, xlabel_text: str = '% of RefSeq sequence contained in construct', grid_alpha: float = 0.3, filename: str = 'ridgeline_plot')[source]

Bases: object

Aesthetics for the ridgeline plot.

__init__(figsize: list[float] = <factory>, overlap: float = 0.1, scale: float = 1.5, fill_alpha: float = 0.5, edgecolor: str = 'black', edge_linewidth: float = 1.5, baseline_linewidth: float = 0.5, baseline_alpha: float = 0.3, ytick_fontsize: int = 20, title_fontsize: int = 22, title_fontweight: str = 'bold', title_color_davis: str = 'black', title_color_pkis2: str = 'black', xtick_fontsize: int = 18, xlabel_fontsize: int = 20, xlabel_text: str = '% of RefSeq sequence contained in construct', grid_alpha: float = 0.3, filename: str = 'ridgeline_plot') → None

baseline_alpha: float = 0.3

baseline_linewidth: float = 0.5

edge_linewidth: float = 1.5

edgecolor: str = 'black'

figsize: list[float]

filename: str = 'ridgeline_plot'

fill_alpha: float = 0.5

grid_alpha: float = 0.3

overlap: float = 0.1

scale: float = 1.5

title_color_davis: str = 'black'

title_color_pkis2: str = 'black'

title_fontsize: int = 22

title_fontweight: str = 'bold'

xlabel_fontsize: int = 20

xlabel_text: str = '% of RefSeq sequence contained in construct'

xtick_fontsize: int = 18

ytick_fontsize: int = 20

class mkt.databases.plot_config.SequenceSchematicConfig(figsize: list[float] = <factory>, rect_height: float = 0.6, gap_color: str = 'white', ellipsis_color: str = '#888888', ellipsis_fontsize: int = 10, label_fontsize: int = 10, title_fontsize: int = 12, title_fontweight: str = 'bold', panel_title_fontsize: int = 11, panel_title_fontweight: str = 'bold', n_show_start: int = 40, n_show_end: int = 20, n_ellipsis: int = 5, filename: str = 'sequence_input_schematic')[source]

Bases: object

Aesthetics for the sequence input schematic.

__init__(figsize: list[float] = <factory>, rect_height: float = 0.6, gap_color: str = 'white', ellipsis_color: str = '#888888', ellipsis_fontsize: int = 10, label_fontsize: int = 10, title_fontsize: int = 12, title_fontweight: str = 'bold', panel_title_fontsize: int = 11, panel_title_fontweight: str = 'bold', n_show_start: int = 40, n_show_end: int = 20, n_ellipsis: int = 5, filename: str = 'sequence_input_schematic') → None

ellipsis_color: str = '#888888'

ellipsis_fontsize: int = 10

figsize: list[float]

filename: str = 'sequence_input_schematic'

gap_color: str = 'white'

label_fontsize: int = 10

n_ellipsis: int = 5

n_show_end: int = 20

n_show_start: int = 40

panel_title_fontsize: int = 11

panel_title_fontweight: str = 'bold'

rect_height: float = 0.6

title_fontsize: int = 12

title_fontweight: str = 'bold'

class mkt.databases.plot_config.StackedBarchartConfig(figsize_width_per_source: float = 12, figsize_height: float = 7, layout_nrows: int = 1, stack_color_true: str = '#d3d3d3', stack_color_false: str = '#505050', bar_edgecolor: str = 'black', bar_linewidth: float = 0.5, bar_alpha: float = 1.0, pct_label_fontsize: int = 20, pct_label_fontweight: str = 'bold', pct_label_min_threshold: float = 5, xtick_fontsize: int = 16, xlabel_fontsize: int = 24, ylabel_fontsize: int = 24, title_fontsize: int = 26, title_fontweight: str = 'bold', ytick_fontsize: int = 18, ylim_max: float = 105, legend_fontsize: int = 20, legend_title_fontsize: int = 20, legend_bbox_y: float = -0.1, bottom_adjust: float = 0.2, title_color_davis: str = 'black', title_color_pkis2: str = 'black', filename: str = 'stacked_barchart')[source]

Bases: object

Aesthetics for the stacked bar chart.

__init__(figsize_width_per_source: float = 12, figsize_height: float = 7, layout_nrows: int = 1, stack_color_true: str = '#d3d3d3', stack_color_false: str = '#505050', bar_edgecolor: str = 'black', bar_linewidth: float = 0.5, bar_alpha: float = 1.0, pct_label_fontsize: int = 20, pct_label_fontweight: str = 'bold', pct_label_min_threshold: float = 5, xtick_fontsize: int = 16, xlabel_fontsize: int = 24, ylabel_fontsize: int = 24, title_fontsize: int = 26, title_fontweight: str = 'bold', ytick_fontsize: int = 18, ylim_max: float = 105, legend_fontsize: int = 20, legend_title_fontsize: int = 20, legend_bbox_y: float = -0.1, bottom_adjust: float = 0.2, title_color_davis: str = 'black', title_color_pkis2: str = 'black', filename: str = 'stacked_barchart') → None

bar_alpha: float = 1.0

bar_edgecolor: str = 'black'

bar_linewidth: float = 0.5

bottom_adjust: float = 0.2

figsize_height: float = 7

figsize_width_per_source: float = 12

filename: str = 'stacked_barchart'

layout_nrows: int = 1

legend_bbox_y: float = -0.1

legend_fontsize: int = 20

legend_title_fontsize: int = 20

pct_label_fontsize: int = 20

pct_label_fontweight: str = 'bold'

pct_label_min_threshold: float = 5

stack_color_false: str = '#505050'

stack_color_true: str = '#d3d3d3'

title_color_davis: str = 'black'

title_color_pkis2: str = 'black'

title_fontsize: int = 26

title_fontweight: str = 'bold'

xlabel_fontsize: int = 24

xtick_fontsize: int = 16

ylabel_fontsize: int = 24

ylim_max: float = 105

ytick_fontsize: int = 18

class mkt.databases.plot_config.UpsetPlotConfig(figsize: list[float] = <factory>, dict_colors: dict = <factory>, element_size: float | None = None, intersection_plot_elements: int = 6, totals_plot_elements: int = 2, tighten_totals_gap: bool = False, totals_gap_margin: float = 0.01, cap_intersection_ylim: bool = False, pct_label_fontsize: int = 8, count_label_fontsize: int = 8, filename: str = 'upset_plot')[source]

Bases: object

Aesthetics for the KinaseInfo source-coverage upset plot.

Defaults reproduce the original (pre-config) figure for backwards compatibility. Use preprint_2026() for the smaller publication size.

__init__(figsize: list[float] = <factory>, dict_colors: dict = <factory>, element_size: float | None = None, intersection_plot_elements: int = 6, totals_plot_elements: int = 2, tighten_totals_gap: bool = False, totals_gap_margin: float = 0.01, cap_intersection_ylim: bool = False, pct_label_fontsize: int = 8, count_label_fontsize: int = 8, filename: str = 'upset_plot') → None

cap_intersection_ylim: bool = False

count_label_fontsize: int = 8

dict_colors: dict

element_size: float | None = None

figsize: list[float]

filename: str = 'upset_plot'

intersection_plot_elements: int = 6

pct_label_fontsize: int = 8

classmethod preprint_2026() → UpsetPlotConfig[source]

~5 x 3.5 in plot-area variant for the 2026 preprint figures.

element_size is tuned empirically (with intersection_plot_elements / totals_plot_elements) so the upset grid renders ~5 x 3.5 in rather than the near-square default; the figure is saved tight-cropped.

tighten_totals_gap: bool = False

totals_gap_margin: float = 0.01

totals_plot_elements: int = 2

class mkt.databases.plot_config.VennDiagramConfig(figsize: list[float] = <factory>, circle_alpha: float = 0.6, intersection_color: str = 'lightgray', intersection_alpha: float = 0.4, set_label_fontsize: int = 16, set_label_fontweight: str = 'bold', subset_label_fontsize: int = 14, title_fontsize: int = 22, title_fontweight: str = 'bold', filename: str = 'venn_diagram')[source]

Bases: object

Aesthetics for the Venn diagram.

__init__(figsize: list[float] = <factory>, circle_alpha: float = 0.6, intersection_color: str = 'lightgray', intersection_alpha: float = 0.4, set_label_fontsize: int = 16, set_label_fontweight: str = 'bold', subset_label_fontsize: int = 14, title_fontsize: int = 22, title_fontweight: str = 'bold', filename: str = 'venn_diagram') → None

circle_alpha: float = 0.6

figsize: list[float]

filename: str = 'venn_diagram'

intersection_alpha: float = 0.4

intersection_color: str = 'lightgray'

set_label_fontsize: int = 16

set_label_fontweight: str = 'bold'

subset_label_fontsize: int = 14

title_fontsize: int = 22

title_fontweight: str = 'bold'