visualization.individual_trajectory

Visualization methods for individual simulators.

Module Attributes

READDY_SAVED_FRAMES

Number of saved frames for ReaDDy simulations.

BOX_SIZE

Bounding box size for individual simulator trajectory.

Functions

visualize_individual_cytosim_trajectories(...)

Visualize individual Cytosim simulations for select conditions and replicates.

visualize_individual_cytosim_trajectory(...)

Save a Simularium file for a single Cytosim trajectory with plots and spatial annotations.

visualize_individual_readdy_trajectories(...)

Visualize individual ReaDDy simulations for select conditions and replicates.

visualize_individual_readdy_trajectory(...)

Save a Simularium file for a single ReaDDy trajectory with plots and spatial annotations.
READDY_SAVED_FRAMES: int = 1000

Number of saved frames for ReaDDy simulations.

BOX_SIZE: ndarray = array([600., 600., 600.])

Bounding box size for individual simulator trajectory.

visualize_individual_readdy_trajectory(bucket: str, series_name: str, series_key: str, rep_ix: int, n_timepoints: int, n_monomer_points: int, total_steps: int, temp_path: str, metrics: list[CompressionMetric], metrics_data: DataFrame) → None[source]

Save a Simularium file for a single ReaDDy trajectory with plots and spatial annotations.

Parameters:

  • bucket – Name of S3 bucket for input and output files.

  • series_name – Name of simulation series.

  • series_key – Combination of series and condition names.

  • rep_ix – Replicate index.

  • n_timepoints – Number of equally spaced timepoints to visualize.

  • n_monomer_points – Number of equally spaced monomer points to visualize.

  • total_steps – Total number of steps for each simulation key.

  • temp_path – Local path for saving visualization output files.

  • metrics – List of metrics to include in visualization plots.

  • metrics_data – Calculated compression metrics data.

visualize_individual_readdy_trajectories(bucket: str, series_name: str, condition_keys: list[str], n_replicates: int, n_timepoints: int, n_monomer_points: int, total_steps: dict[str, int], temp_path: str, metrics: list[CompressionMetric] | None = None, recalculate: bool = True) → None[source]

Visualize individual ReaDDy simulations for select conditions and replicates.

Parameters:

  • bucket – Name of S3 bucket for input and output files.

  • series_name – Name of simulation series.

  • condition_keys – List of condition keys.

  • n_replicates – Number of simulation replicates.

  • n_timepoints – Number of equally spaced timepoints to visualize.

  • n_monomer_points – Number of equally spaced monomer points to visualize.

  • total_steps – Total number of steps for each simulation key.

  • temp_path – Local path for saving visualization output files.

  • metrics – List of metrics to include in visualization plots.

  • recalculate – True to recalculate visualization files, False otherwise.

visualize_individual_cytosim_trajectory(bucket: str, series_name: str, series_key: str, index: int, n_timepoints: int, temp_path: str, metrics: list[CompressionMetric], metrics_data: DataFrame) → None[source]

Save a Simularium file for a single Cytosim trajectory with plots and spatial annotations.

Parameters:

  • bucket – Name of S3 bucket for input and output files.

  • series_name – Name of simulation series.

  • series_key – Combination of series and condition names.

  • index – Simulation replicate index.

  • n_timepoints – Number of equally spaced timepoints to visualize.

  • temp_path – Local path for saving visualization output files.

  • metrics – List of metrics to include in visualization plots.

  • metrics_data – Calculated compression metrics data.

visualize_individual_cytosim_trajectories(bucket: str, series_name: str, condition_keys: list[str], random_seeds: list[int], n_timepoints: int, temp_path: str, metrics: list[CompressionMetric] | None = None, recalculate: bool = True) → None[source]

Visualize individual Cytosim simulations for select conditions and replicates.

Parameters:

  • bucket – Name of S3 bucket for input and output files.

  • series_name – Name of simulation series.

  • condition_keys – List of condition keys.

  • random_seeds – Random seeds for simulations.

  • n_timepoints – Number of equally spaced timepoints to visualize.

  • temp_path – Local path for saving visualization output files.

  • metrics – List of metrics to include in visualization plots.

  • recalculate – True to recalculate visualization files, False otherwise.