plot_cell_shapes#

Workflow for plotting cell shapes.

Working location structure:

(name)
├── groups
│   └── groups.CELL_SHAPES
│       ├── (name).feature_correlations.(key).(region).csv
│       ├── (name).feature_distributions.(feature).json
│       ├── (name).mode_correlations.csv
│       ├── (name).population_counts.(tick).csv
│       ├── (name).population_stats.json
│       ├── (name).shape_average.(key).(projection).json
│       ├── (name).shape_errors.json
│       ├── (name).shape_modes.(key).(region).(mode).(projection).json
│       └── (name).variance_explained.csv
└── plots
    └── plots.CELL_SHAPES
        ├── (name).feature_correlations.(key).(region).png
        ├── (name).feature_distributions.(feature).png
        ├── (name).mode_correlations.(key).(key).png
        ├── (name).population_counts.(tick).png
        ├── (name).population_stats.png
        ├── (name).shape_average.(key).(projection).svg
        ├── (name).shape_errors.png
        ├── (name).shape_modes.(key).(region).(mode).(projection).(point).svg
        └── (name).variance_explained.png

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

Flows

`run_flow`	Main plot cell shapes flow.
`run_flow_plot_feature_correlations`	Plot cell shapes subflow for feature correlations.
`run_flow_plot_feature_distributions`	Plot cell shapes subflow for feature distributions.
`run_flow_plot_mode_correlations`	Plot cell shapes subflow for mode correlations.
`run_flow_plot_population_counts`	Plot cell shapes subflow for population counts.
`run_flow_plot_population_stats`	Plot cell shapes subflow for population stats.
`run_flow_plot_shape_average`	Plot cell shapes subflow for shape average.
`run_flow_plot_shape_errors`	Plot cell shapes subflow for shape errors.
`run_flow_plot_shape_modes`	Plot cell shapes subflow for shape modes.
`run_flow_plot_variance_explained`	Plot cell shapes subflow for variance explained.

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

Main plot cell shapes flow.

Calls the following subflows, if the plot is specified:

run_flow_plot_feature_correlations()
run_flow_plot_feature_distributions()
run_flow_plot_mode_correlations()
run_flow_plot_population_counts()
run_flow_plot_population_stats()
run_flow_plot_shape_average()
run_flow_plot_shape_errors()
run_flow_plot_shape_modes()
run_flow_plot_variance_explained()

run_flow_plot_feature_correlations(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigFeatureCorrelations) → None[source]#: Plot cell shapes subflow for feature correlations.

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

run_flow_plot_mode_correlations(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigModeCorrelations) → None[source]#: Plot cell shapes subflow for mode correlations.

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

run_flow_plot_population_stats(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigPopulationStats) → None[source]#: Plot cell shapes subflow for population stats.

run_flow_plot_shape_average(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigShapeAverage) → None[source]#: Plot cell shapes subflow for shape average.

run_flow_plot_shape_errors(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigShapeErrors) → None[source]#: Plot cell shapes subflow for shape errors.

run_flow_plot_shape_modes(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigShapeModes) → None[source]#: Plot cell shapes subflow for shape modes.

run_flow_plot_variance_explained(context: ContextConfig, series: SeriesConfig, parameters: ParametersConfigVarianceExplained) → None[source]#: Plot cell shapes subflow for variance explained.

Configs

`ContextConfig`	Context configuration for plot cell shapes flow.
`ParametersConfig`	Parameter configuration for plot cell shapes flow.
`ParametersConfigFeatureCorrelations`	Parameter configuration for plot cell shapes subflow - feature correlations.
`ParametersConfigFeatureDistributions`	Parameter configuration for plot cell shapes subflow - feature distributions.
`ParametersConfigModeCorrelations`	Parameter configuration for plot cell shapes subflow - mode correlations.
`ParametersConfigPopulationCounts`	Parameter configuration for plot cell shapes subflow - population counts.
`ParametersConfigPopulationStats`	Parameter configuration for plot cell shapes subflow - population stats.
`ParametersConfigShapeAverage`	Parameter configuration for plot cell shapes subflow - shape average.
`ParametersConfigShapeErrors`	Parameter configuration for plot cell shapes subflow - shape errors.
`ParametersConfigShapeModes`	Parameter configuration for plot cell shapes subflow - shape modes.
`ParametersConfigVarianceExplained`	Parameter configuration for plot cell shapes subflow - variance explained.
`SeriesConfig`	Series configuration for plot cell shapes flow.

class ContextConfig[source]#

Context configuration for plot cell shapes flow.

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

class ParametersConfig[source]#

Parameter configuration for plot cell shapes flow.

plots: list[str]#: List of cell shape plots.

feature_correlations: ParametersConfigFeatureCorrelations = ParametersConfigFeatureCorrelations(properties=['volume', 'height', 'area', 'axis_major_length', 'axis_minor_length', 'eccentricity', 'perimeter'], regions=['DEFAULT'], components=8)#: Parameters for plot feature correlations subflow.

feature_distributions: ParametersConfigFeatureDistributions = ParametersConfigFeatureDistributions(properties=['volume', 'height'], regions=['(region)'], components=8)#: Parameters for plot feature distributions subflow.

mode_correlations: ParametersConfigModeCorrelations = ParametersConfigModeCorrelations(components=8)#: Parameters for plot mode correlations subflow.

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

population_stats: ParametersConfigPopulationStats = ParametersConfigPopulationStats()#: Parameters for plot population stats subflow.

shape_average: ParametersConfigShapeAverage = ParametersConfigShapeAverage(projections=['top', 'side1', 'side2'], box=(100, 100), scale=1)#: Parameters for plot shape average subflow.

shape_errors: ParametersConfigShapeErrors = ParametersConfigShapeErrors()#: Parameters for plot shape errors subflow.

shape_modes: ParametersConfigShapeModes = ParametersConfigShapeModes(regions=['(region)'], components=8, projections=['top', 'side1', 'side2'], point=0, box=(100, 100), scale=1, colors={'DEFAULT': '#FF00FF', 'NUCLEUS': '#00FFFF'})#: Parameters for plot shape modes subflow.

variance_explained: ParametersConfigVarianceExplained = ParametersConfigVarianceExplained(components=8, colors=['#7F3C8D', '#11A579', '#3969AC', '#F2B701', '#E73F74', '#80BA5A', '#E68310', '#008695', '#CF1C90', '#f97b72', '#4b4b8f', '#A5AA99'])#: Parameters for plot variance explained subflow.

class ParametersConfigFeatureCorrelations[source]#

Parameter configuration for plot cell shapes subflow - feature correlations.

properties: list[str]#: List of shape properties.

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

components: int = 8#: Number of principal components (i.e. shape modes).

class ParametersConfigFeatureDistributions[source]#

Parameter configuration for plot cell shapes subflow - feature distributions.

properties: list[str]#: List of shape properties.

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

components: int = 8#: Number of principal components (i.e. shape modes).

class ParametersConfigModeCorrelations[source]#

Parameter configuration for plot cell shapes subflow - mode correlations.

components: int = 8#: Number of principal components (i.e. shape modes).

class ParametersConfigPopulationCounts[source]#

Parameter configuration for plot cell shapes subflow - population counts.

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

class ParametersConfigPopulationStats[source]#: Parameter configuration for plot cell shapes subflow - population stats.

class ParametersConfigShapeAverage[source]#

Parameter configuration for plot cell shapes subflow - shape average.

projections: list[str]#: List of shape projections.

box: tuple[int, int]#: Size of bounding box.

scale: float = 1#: Scaling for image.

class ParametersConfigShapeErrors[source]#: Parameter configuration for plot cell shapes subflow - shape errors.

class ParametersConfigShapeModes[source]#

Parameter configuration for plot cell shapes subflow - shape modes.

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

components: int = 8#: Number of principal components (i.e. shape modes).

projections: list[str]#: List of shape projections.

point: float = 0#: Selected shape mode map point.

box: tuple[int, int]#: Size of bounding box.

scale: float = 1#: Scaling for image.

colors: dict[str, str]#: Colors for each region.

class ParametersConfigVarianceExplained[source]#

Parameter configuration for plot cell shapes subflow - variance explained.

components: int = 8#: Number of principal components (i.e. shape modes).

colors: list[str]#: Colors for each key.

class SeriesConfig[source]#

Series configuration for plot cell shapes flow.

name: str#: Name of the simulation series.

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