plot_basic_metrics#

Workflow for plotting basic metrics.

Working location structure:

(name)
├── groups
│   └── groups.BASIC_METRICS
│       ├── (name).metrics_bins.(key).(seed).(tick).(metric).csv
│       ├── (name).metrics_distributions.(metric).json
│       ├── (name).metrics_individuals.(key).(seed).(metric).json
│       ├── (name).metrics_spatial.(key).(seed).(tick).(metric).csv
│       ├── (name).metrics_temporal.(key).(metric).json
│       └── (name).population_counts.(tick).csv
└── plots
    └── plots.BASIC_METRICS
        ├── (name).metrics_bins.(key).(seed).(tick).(metric).png
        ├── (name).metrics_distributions.(metric).png
        ├── (name).metrics_individuals.(key).(seed).(metric).png
        ├── (name).metrics_spatial.(key).(seed).(tick).(metric).png
        ├── (name).metrics_temporal.(key).(metric).png
        └── (name).population_counts.(tick).png

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

Flows

`run_flow`	Main plot basic metrics flow.
`run_flow_plot_metrics_bins`	Plot basic metrics subflow for binned metrics.
`run_flow_plot_metrics_distributions`	Plot basic metrics subflow for metrics distributions.
`run_flow_plot_metrics_individuals`	Plot basic metrics subflow for individual metrics.
`run_flow_plot_metrics_spatial`	Plot basic metrics subflow for spatial metrics.
`run_flow_plot_metrics_temporal`	Plot basic metrics subflow for temporal metrics.
`run_flow_plot_population_counts`	Plot basic metrics subflow for population counts.

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

Main plot basic metrics flow.

Calls the following subflows, if the plot is specified:

run_flow_plot_metrics_bins()
run_flow_plot_metrics_distributions()
run_flow_plot_metrics_individuals()
run_flow_plot_metrics_spatial()
run_flow_plot_metrics_temporal()
run_flow_plot_population_stats()

run_flow_plot_metrics_bins(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsBins) → None[source]#: Plot basic metrics subflow for binned metrics.

run_flow_plot_metrics_distributions(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsDistributions) → None[source]#: Plot basic metrics subflow for metrics distributions.

run_flow_plot_metrics_individuals(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsIndividuals) → None[source]#: Plot basic metrics subflow for individual metrics.

run_flow_plot_metrics_spatial(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsSpatial) → None[source]#: Plot basic metrics subflow for spatial metrics.

run_flow_plot_metrics_temporal(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigMetricsTemporal) → None[source]#: Plot basic metrics subflow for temporal metrics.

run_flow_plot_population_counts(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigPopulationCounts) → None[source]#: Plot basic metrics subflow for population counts.

Configs

`ContextConfig`	Context configuration for plot basic metrics flow.
`ParametersConfig`	Parameter configuration for plot basic metrics flow.
`ParametersConfigMetricsBins`	Parameter configuration for plot basic metrics subflow - metrics bins.
`ParametersConfigMetricsDistributions`	Parameter configuration for plot basic metrics subflow - metrics distributions.
`ParametersConfigMetricsIndividuals`	Parameter configuration for plot basic metrics subflow - metrics individuals.
`ParametersConfigMetricsSpatial`	Parameter configuration for plot basic metrics subflow - metrics spatial.
`ParametersConfigMetricsTemporal`	Parameter configuration for plot basic metrics subflow - metrics temporal.
`ParametersConfigPopulationCounts`	Parameter configuration for plot basic metrics subflow - population counts.
`SeriesConfig`	Series configuration for plot basic metrics flow.

class ContextConfig[source]#

Context configuration for plot basic metrics flow.

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

class ParametersConfig[source]#

Parameter configuration for plot basic metrics flow.

plots: list[str]#: List of basic metric plots.

metrics_bins: ParametersConfigMetricsBins = ParametersConfigMetricsBins(metrics=['count', 'volume', 'height'], seed=0, ticks=[0], scale=1)#: Parameters for plot metrics bins subflow.

metrics_distributions: ParametersConfigMetricsDistributions = ParametersConfigMetricsDistributions(metrics=['phase', 'volume', 'height'], phases=['PROLIFERATIVE_G1', 'PROLIFERATIVE_S', 'PROLIFERATIVE_G2', 'PROLIFERATIVE_M', 'APOPTOTIC_EARLY', 'APOPTOTIC_LATE'], regions=['DEFAULT'])#: Parameters for plot metrics distributions subflow.

metrics_individuals: ParametersConfigMetricsIndividuals = ParametersConfigMetricsIndividuals(metrics=['volume', 'height'], seed=0, regions=['DEFAULT'], phase_colors={'PROLIFERATIVE_G1': '#7F3C8D', 'PROLIFERATIVE_S': '#11A579', 'PROLIFERATIVE_G2': '#3969AC', 'PROLIFERATIVE_M': '#F2B701', 'APOPTOTIC_EARLY': '#E73F74', 'APOPTOTIC_LATE': '#80BA5A'})#: Parameters for plot metrics individuals subflow.

metrics_spatial: ParametersConfigMetricsSpatial = ParametersConfigMetricsSpatial(metrics=['population', 'phase', 'volume', 'height'], seeds=[0], regions=['DEFAULT'], ticks=[0], phase_colors={'PROLIFERATIVE_G1': '#7F3C8D', 'PROLIFERATIVE_S': '#11A579', 'PROLIFERATIVE_G2': '#3969AC', 'PROLIFERATIVE_M': '#F2B701', 'APOPTOTIC_EARLY': '#E73F74', 'APOPTOTIC_LATE': '#80BA5A'}, population_colors={1: '#7F3C8D'})#: Parameters for plot metrics spatial subflow.

metrics_temporal: ParametersConfigMetricsTemporal = ParametersConfigMetricsTemporal(metrics=['count', 'population', 'phase', 'volume', 'height'], regions=['DEFAULT'], populations=[1], phases=['PROLIFERATIVE_G1', 'PROLIFERATIVE_S', 'PROLIFERATIVE_G2', 'PROLIFERATIVE_M', 'APOPTOTIC_EARLY', 'APOPTOTIC_LATE'])#: Parameters for plot metrics temporal subflow.

population_counts: ParametersConfigPopulationCounts = ParametersConfigPopulationCounts(tick=0)#: Parameters for plot population counts subflow.

class ParametersConfigMetricsBins[source]#

Parameter configuration for plot basic metrics subflow - metrics bins.

metrics: list[str]#: List of bin metrics.

seed: int = 0#: Simulation seed to use for plotting bin metrics.

ticks: list[int]#: Simulation ticks to use for plotting bin metrics.

scale: float = 1#: Metric bin scaling.

class ParametersConfigMetricsDistributions[source]#

Parameter configuration for plot basic metrics subflow - metrics distributions.

metrics: list[str]#: List of distribution metrics.

phases: list[str]#: List of cell cycle phases.

regions: list[str]#: List of subcellular regions.

class ParametersConfigMetricsIndividuals[source]#

Parameter configuration for plot basic metrics subflow - metrics individuals.

metrics: list[str]#: List of individual metrics.

seed: int = 0#: Simulation seed to use for plotting individual metrics.

regions: list[str]#: List of subcellular regions.

phase_colors: dict[str, str]#: Colors for each cell cycle phase.

class ParametersConfigMetricsSpatial[source]#

Parameter configuration for plot basic metrics subflow - metrics spatial.

metrics: list[str]#: List of spatial metrics.

seeds: list[int]#: Simulation seeds to use for plotting spatial metrics.

regions: list[str]#: List of subcellular regions.

ticks: list[int]#: Simulation ticks to use for plotting spatial metrics.

phase_colors: dict[str, str]#: Colors for each cell cycle phase.

population_colors: dict[int, str]#: Colors for each cell population.

class ParametersConfigMetricsTemporal[source]#

Parameter configuration for plot basic metrics subflow - metrics temporal.

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

regions: list[str]#: List of subcellular regions.

populations: list[int]#: List of cell populations.

phases: list[str]#: List of cell cycle phases.

class ParametersConfigPopulationCounts[source]#

Parameter configuration for plot basic metrics subflow - population counts.

tick: int = 0#: Simulation tick to use for plotting population counts.

class SeriesConfig[source]#

Series configuration for plot basic metrics flow.

name: str#: Name of the simulation series.

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