Example Usage

FlyEye Analysis provides a wide range of functionality for analyzing the expression data contained in .silhouette files. A very brief survey of some basic operations is provided below. For detailed usage instructions please see the documentation.

Loading Silhouette Data

See Getting Started for input data requirements.

To load an individual eye disc:

>>> from flyeye.data import Disc
>>> disc = Disc.from_silhouette(path_to_silhouette_file)

To load an entire experiment:

>>> from flyeye.data import Experiment
>>> experiment = Experiment(path_to_experiment)

Querying measurements

Select by disc ID:

>>> disc_id = 2
>>> disc = experiment.discs[disc_id]

Select by cell type:

>>> cell_type = 'pre'
>>> cells = disc.select_cell_type(cell_type)

Select by developmental time:

>>> tmin, tmax = 5, 15
>>> cells = disc.select_by_position(tmin=tmin, tmax=tmax)

Visualizing Dynamics

Plot expression dynamics:

>>> reporter_channel = 'ch0'
>>> cells.plot_dynamics(reporter_channel)

Plot expression heterogeneity dynamics:

>>> reporter_channel = 'ch0'
>>> fluctuations_channel = reporter_channel + '_flux'
>>> cells.plot_dynamics(fluctuations_channel)

Additional Examples

For additional usage examples, please refer to our study of Pnt and Yan expression during photoreceptor specification.