Visualization options (biomass.plotting
)
Figure properties for visualizing time-course simulations and sensitivity analysis results.
Example code: Nakakuki_Cell_2010
- class biomass.plotting.MultipleObservables(cm)
Visualization options for time-course simulation (multi-observables).
- fname
Output file name.
- Type:
str
- figsize
Figure size.
- Type:
tuple (default: (4, 3))
- observables
Specify which observables to plot.
- Type:
list of strings
- condition
Specify which simulation condition to be plotted.
- Type:
str, optional
- xlim
Set the x limits of the current axes.
- Type:
tuple
- xticks
Set the current tick locations of the x-axis.
- Type:
list (default:
None
)
- xlabel
Set the label for the x-axis.
- Type:
str (default: ‘Time’)
- ylim
Set the y limits of the current axes.
- Type:
tuple
- yticks
Set the current tick locations of the y-axis.
- Type:
list (default:
None
)
- ylabel
Set the label for the y-axis.
- Type:
str (default: ‘’)
- legend_kws
Keyword arguments to pass to
matplotlib.pyplot.legend()
.- Type:
dict, optional
- cmap
Set colormap.
- Type:
list or tuple
- shape
Set markers.
- Type:
list or tuple of strings (default:
matplotlib.lines.Line2D.filled_markers
)
- class biomass.plotting.SensitivityOptions(cm)
Bar plot visualization options for sensitivity analysis results. When setting style to ‘heatmap’, change plotting options via
clustermap_kws
.- figsize
Figure size.
- Type:
tuple
- width
The width(s) of the bars when choosing style == ‘barplot’.
- Type:
float
- legend_kws
Keyword arguments to pass to
matplotlib.pyplot.legend()
.- Type:
dict, optional
- cmap
Set colormap.
- Type:
list or tuple
- class biomass.plotting.SingleObservable(cm, obs_name)
Visualization options for time-course simulation (single-observable).
- divided_by
Convert time unit. (e.g. sec -> min).
- Type:
int or float (default: 1)
- figsize
Width, height in inches.
- Type:
tuple (default: (4, 3))
- xlim
Set the x limits of the current axes.
- Type:
tuple
- xticks
Set the current tick locations of the x-axis.
- Type:
list (default:
None
)
- xlabel
Set the label for the x-axis.
- Type:
str (default: ‘Time’)
- ylim
Set the y limits of the current axes.
- Type:
tuple
- yticks
Set the current tick locations of the y-axis.
- Type:
list (default:
None
)
- ylabel
Set the label for the y-axis.
- Type:
str (default: obs_name.replace(‘_’, ‘ ‘))
- exp_data
if False, experimental data will not be shown.
- Type:
bool (default: True)
- legend_kws
Keyword arguments to pass to
matplotlib.pyplot.legend()
.- Type:
dict, optional
- cmap
Set colormap.
- Type:
list or tuple
- shape
Set markers.
- Type:
list or tuple of strings (default:
matplotlib.lines.Line2D.filled_markers
)
- dont_show
Set conditions you don’t want to plot.
- Type:
list of strings