vivarium.plots.colonies module

Colony Plotting Tools

This module contains tools to help you plot colony data.

vivarium.plots.colonies.AREA_PATH = ('surface_area',)

Key for surface area in path timeseries

vivarium.plots.colonies.AXIS_RATIO_PATH = '(Major Axis) / (Minor Axis)'

Key to which the ratio of major axis to minor axis is written in the path timeseries

vivarium.plots.colonies.CIRCUMFERENCE_AREA_RATIO_PATH = 'circumference / surface_area'

Key to which the cirumference-to-area ratio will be written in the path timeseries

vivarium.plots.colonies.CIRCUMFERENCE_PATH = ('circumference',)

Key for circumference in path timeseries

vivarium.plots.colonies.MAJOR_AXIS_PATH = ('major_axis',)

Key for major axis in path timeseries

vivarium.plots.colonies.MINOR_AXIS_PATH = ('minor_axis',)

Key for minor axis in path timeseries

vivarium.plots.colonies.NUM_COLONIES_PATH = 'Number of Colonies'

Key to which the number of colonies is written in the path timeseries

vivarium.plots.colonies.plot_colony_metrics(path_ts, title_size=16, tick_label_size=12, max_cols=5)[source]

Plot colony metrics over time.

Metric mean is plotted with SEM error bands.

Parameters

  • path_ts (dict) – Path timeseries of the data to plot. Each item in the dictionary should have as its key the path and as its value a list of values for each timepoint. Each value should be a list of metric values, one entry per colony. The dictionary should have one additional key, time, whose value is a list of times for each timepoint.

  • title_size (int) – Font size for the title of each plot

  • tick_label_size (int) – Font size for each plot’s axis tick labels.

  • max_cols (int) – The maximum number of columns. We add columns until we hit this limit, and only then do we add rows.

Returns

The plot as a Figure object.

Return type

matplotlib.figure.Figure

vivarium.plots.colonies.plot_metric_across_experiments(path_ts_dict, path, title=None, xlabel='time (s)', ylabel=None, title_size=16, tick_label_size=12)[source]

Overlay plots of a single metric from different experiments.

Parameters

  • path_ts_dict (dict) – Map from the string to use as the label for the experiment in the legend to that experiment’s path timeseries.

  • path (tuple) – Path to plot. Should be a key in each value of path_ts_dict.

  • title (str) – Plot title. If None, no title is set.

  • xlabel (str) – X-axis label. If None, no label is set.

  • ylabel (str) – Y-axis label. If None, no label is set.

  • title_size (float) – Font size for plot and axis titles.

  • tick_label_size (float) – Font size for tick labels.

Returns

The figure with the plot.