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