biosimulators_utils.viz package

Subpackages

Submodules

biosimulators_utils.viz.data_model module

Data model for plots

Author

Jonathan Karr <karr@mssm.edu>

Date

2020-12-06

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

class biosimulators_utils.viz.data_model.VizFormat(value)[source]

Bases: str, enum.Enum

Format of a report

jpg = 'jpg'[source]
pdf = 'pdf'[source]
png = 'png'[source]
svg = 'svg'[source]

biosimulators_utils.viz.io module

Methods for generating SED plots

Author

Jonathan Karr <karr@mssm.edu>

Date

2020-12-23

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.viz.io.write_plot_2d(plot, data_generator_results, base_path, rel_path, format=VizFormat.pdf, style='seaborn-paper')[source]

Generate a 2D plot

Parameters
  • plot (Plot2D) – description of plot

  • data_generator_results (DataGeneratorResults) – results of data generators

  • base_path (str) – base path to save plot

  • rel_path (str) – path to save results relative to base_path

  • format (VizFormat, optional) – format

  • style (str, optional) – matplotlib style

biosimulators_utils.viz.io.write_plot_3d(plot, data_generator_results, base_path, rel_path, format=VizFormat.pdf, style='seaborn-paper', colormaps=[<matplotlib.colors.ListedColormap object>, <matplotlib.colors.ListedColormap object>, <matplotlib.colors.ListedColormap object>, <matplotlib.colors.ListedColormap object>, <matplotlib.colors.ListedColormap object>])[source]

Generate a 3D plot

Parameters
  • plot (Plot3D) – description of plot

  • data_generator_results (DataGeneratorResults) – results of data generators

  • base_path (str) – base path to save plot

  • rel_path (str) – path to save results relative to base_path

  • format (VizFormat, optional) – format

  • style (str, optional) – matplotlib style

  • colormaps (list of matplotlib.colors.LinearSegmentedColormap, optional) – colormaps

biosimulators_utils.viz.utils module

Utilities for visualizations

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-07-22

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.viz.utils.cubic_bezier_angle(points, t)[source]

Get the angle of a point along a cubic bezier curve

Parameters
  • points (list of list of float) – control points

  • t (float) – position along the curve [0, 1]

Returns

angle of the curve at point t

Return type

float

biosimulators_utils.viz.utils.cubic_bezier_point(points, t)[source]

Get the coordinate of a point along a cubic bezier curve

Parameters
  • points (list of list of float) – control points

  • t (float) – position along the curve [0, 1]

Returns

position of the curve at point t

Return type

tuple of float

biosimulators_utils.viz.warnings module

Warnings for plots

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-01-20

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

exception biosimulators_utils.viz.warnings.IllogicalVizWarning[source]

Bases: biosimulators_utils.warnings.BioSimulatorsWarning

Warning that a plot is may be illogical (e.g., has mixed axes or scales)