plot_colony_dynamics#

Workflow for plotting colony dynamics.

Working location structure:

(name)
├── groups
│   └── groups.COLONIES
│       ├── (name).feature_distributions.(feature).json
│       ├── (name).feature_temporal.(key).(feature).json
│       ├── (name).neighbor_positions.(key).(seed).(tick).csv
│       └── (name).neighbor_positions.(key).(seed).(tick).(feature).csv
└── plots
    └── plots.COLONIES
        ├── (name).feature_distributions.(feature).png
        ├── (name).feature_temporal.(key).(feature).json
        └── (name).neighbor_positions.(key).(seed).(tick).(feature).png

Plots use grouped data from groups.COLONIES. Plots are saved to plots.COLONIES.

Flows

`run_flow`	Main plot colony dynamics flow.
`run_flow_plot_feature_distributions`	Plot colony dynamics subflow for feature distributions.
`run_flow_plot_feature_temporal`	Plot colony dynamics subflow for temporal features.
`run_flow_plot_neighbor_positions`	Plot colony dynamics subflow for neighbor positions.

run_flow(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfig) → None[source]#

Main plot colony dynamics flow.

Calls the following subflows, if the plot is specified:

run_flow_plot_feature_distributions()
run_flow_plot_feature_temporal()
run_flow_plot_neighbor_positions()

run_flow_plot_feature_distributions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigFeatureDistributions) → None[source]#: Plot colony dynamics subflow for feature distributions.

run_flow_plot_feature_temporal(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigFeatureTemporal) → None[source]#: Plot colony dynamics subflow for temporal features.

run_flow_plot_neighbor_positions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigNeighborPositions) → None[source]#: Plot colony dynamics subflow for neighbor positions.

Configs

`ContextConfig`	Context configuration for plot colony dynamics flow.
`ParametersConfig`	Parameter configuration for plot colony dynamics flow.
`ParametersConfigFeatureDistributions`	Parameter configuration for plot colony dynamics subflow - feature distributions.
`ParametersConfigFeatureTemporal`	Parameter configuration for plot colony dynamics subflow - feature temporal.
`ParametersConfigNeighborPositions`	Parameter configuration for plot colony dynamics subflow - neighbor positions.
`SeriesConfig`	Series configuration for plot colony dynamics flow.

class ContextConfig[source]#

Context configuration for plot colony dynamics flow.

working_location: str#: Location for input and output files (local path or S3 bucket).

class ParametersConfig[source]#

Parameter configuration for plot colony dynamics flow.

plots: list[str]#: List of colony dynamics plots.

feature_distributions: ParametersConfigFeatureDistributions = ParametersConfigFeatureDistributions(features=['degree', 'eccentricity', 'degree_centrality', 'closeness_centrality', 'betweenness_centrality'])#: Parameters for plot feature distributions subflow.

feature_temporal: ParametersConfigFeatureTemporal = ParametersConfigFeatureTemporal(features=['degree', 'eccentricity', 'degree_centrality', 'closeness_centrality', 'betweenness_centrality', 'radius', 'diameter'])#: Parameters for plot feature temporal subflow.

neighbor_positions: ParametersConfigNeighborPositions = ParametersConfigNeighborPositions(features=['depth', 'group'], seed=0, ticks=[0], colormaps={'depth': 'magma_r', 'group': 'tab10'})#: Parameters for plot neighbor positions subflow.

class ParametersConfigFeatureDistributions[source]#

Parameter configuration for plot colony dynamics subflow - feature distributions.

features: list[str]#: List of colony features.

class ParametersConfigFeatureTemporal[source]#

Parameter configuration for plot colony dynamics subflow - feature temporal.

features: list[str]#: List of temporal features.

class ParametersConfigNeighborPositions[source]#

Parameter configuration for plot colony dynamics subflow - neighbor positions.

features: list[str]#: List of position features.

seed: int = 0#: Simulation seed to use for plotting neighbor positions.

ticks: list[int]#: Simulation ticks to use for plotting neighbor positions.

colormaps: dict[str, str]#: Colormaps for each feature.

class SeriesConfig[source]#

Series configuration for plot colony dynamics flow.

name: str#: Name of the simulation series.

conditions: list[dict]#: List of series condition dictionaries (must include unique condition “key”).