plot

Visualizations for stratum retention policies.

Functions

mrca_uncertainty_absolute_barplot(...[, ...])	Profile distribution of retained rank spacing under a retention policy.
mrca_uncertainty_relative_barplot(...[, ...])	Profile distribution of retained rank spacing under a retention policy.
policy_panel_plot(stratum_retention_policy, ...)	Holistically sketch stratum retention policy at a particular generation.
strata_retained_frac_lineplot(...[, do_show, ax])	Plot fraction deposited strata that are retained at each generation.
strata_retained_num_lineplot(...[, do_show, ax])	Plot number deposited strata that are retained at each generation.
stratum_retention_dripplot(...[, do_show, ...])	Show history of retained and purged strata at a particular generation.

mrca_uncertainty_absolute_barplot(stratum_retention_policy: Any, num_generations: int, do_show: bool = False, ax: Axes | None = None) → Axes

Profile distribution of retained rank spacing under a retention policy.

Plots absolute uncertainty for MRCA estimation over column ranks (positions) in a hereditary stratigraphic column at a particular generation under a particular stratum retention policy.

Parameters

stratum_retention_policyCallable

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

axmatplotlib/pylab axes, optional

If a valid matplotlib.axes.Axes instance, the plot is drawn in that Axes. By default (None), a new axes is created.

do_showbool, optional

Whether to show() the plot automatically.

mrca_uncertainty_relative_barplot(stratum_retention_policy: Any, num_generations: int, do_show: bool = False, ax: Axes | None = None) → Axes

Profile distribution of retained rank spacing under a retention policy.

Plots relative uncertainty for MRCA estimation over column ranks (positions) in a hereditary stratigraphic column at a particular generation under a particular stratum retention policy.

Parameters

stratum_retention_policyCallable

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

axmatplotlib/pylab axes, optional

If a valid matplotlib.axes.Axes instance, the plot is drawn in that Axes. By default (None), a new axes is created.

do_showbool, optional

Whether to show() the plot automatically.

policy_panel_plot(stratum_retention_policy: Any, num_generations: int, do_show: bool = False, fig: Figure | None = None) → Figure

Holistically sketch stratum retention policy at a particular generation.

Produces a composite multipanel plot.

Parameters

stratum_retention_policyany

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

do_showbool, optional

Whether to show() the plot automatically.

figmatplotlib/pylab figure, optional

If a valid matplotlib.figure.Figure instance, the plot is drawn in that Figure. By default (None), a new figure is created.

strata_retained_frac_lineplot(stratum_retention_policy: Any, num_generations: int, do_show: bool = False, ax: Axes | None = None) → Axes

Plot fraction deposited strata that are retained at each generation.

Parameters

stratum_retention_policyany

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

axmatplotlib/pylab axes, optional

If a valid matplotlib.axes.Axes instance, the plot is drawn in that Axes. By default (None), a new axes is created.

do_showbool, optional

Whether to show() the plot automatically.

strata_retained_num_lineplot(stratum_retention_policy: Callable[[int, int], bool], num_generations: int, do_show: bool = False, ax: Axes | None = None) → Axes

Plot number deposited strata that are retained at each generation.

Parameters

stratum_retention_policyany

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

axmatplotlib/pylab axes, optional

If a valid matplotlib.axes.Axes instance, the plot is drawn in that Axes. By default (None), a new axes is created.

do_showbool, optional

Whether to show() the plot automatically.

stratum_retention_dripplot(stratum_retention_policy: ~typing.Any, num_generations: int, do_show: bool = False, ax: ~matplotlib.axes._axes.Axes | None = None, draw_extant_history: bool = True, draw_extinct_history: bool = True, draw_extinct_placeholders: bool = False, progress_wrap: ~typing.Callable = <function <lambda>>) → Axes

Show history of retained and purged strata at a particular generation.

Plots position of retained strata within a hereditary stratigraphic column over successive depositions under a particular stratum retention policy.

Parameters

stratum_retention_policyany

Object specifying stratum retention policy.

num_generationsint

Number of generations to plot.

do_showbool, optional

Whether to show() the plot automatically.

axmatplotlib/pylab axes, optional

If a valid matplotlib.axes.Axes instance, the plot is drawn in that Axes. By default (None), a new axes is created.

progress_wrapCallable, default identity function

Wrapper applied around generation iterator and row generator for final phylogeny compilation process.

Pass tqdm or equivalent to display progress bars.