sbmlsim.plot

Submodules

Package Contents

Classes

Figure

A figure consists of multiple subplots.

Plot

Plot panel.

Axis

Base class for plotting objects.

SubPlot

A SubPlot is a locate plot in a figure.

Curve

Base class for plotting objects.

ColorType

MarkerType

Generic enumeration.
class sbmlsim.plot.Figure(experiment, sid, name=None, subplots=None, height=None, width=None, num_rows=1, num_cols=1)[source]

Bases: BasePlotObject

A figure consists of multiple subplots.

A reference to the experiment is required, so the plot can resolve the datasets and the simulations.

Parameters

  • sid (str) –

  • name (str) –

  • subplots (List[SubPlot]) –

  • height (float) –

  • width (float) –

  • num_rows (int) –

  • num_cols (int) –

fig_dpi = 72
fig_facecolor = white
fig_subplots_wspace = 0.3
fig_subplots_hspace = 0.3
panel_width = 7
panel_height = 5
fig_titlesize = 25
fig_titleweight = bold
axes_titlesize = 20
axes_titleweight = bold
axes_labelsize = 18
axes_labelweight = bold
xtick_labelsize = 15
ytick_labelsize = 15
legend_fontsize = 13
legend_loc = best
_area_interpolation_points = 300
num_subplots(self)

Number of existing subplots.

num_panels(self)

Number of available spots for plots.

set_title(self, title)
create_plots(self, xaxis=None, yaxis=None, legend=True)

Template function for creating plots

Parameters

  • xaxis (Axis) –

  • yaxis (Axis) –

  • legend (bool) –

Return type

List[Plot]

property plots(self)
get_plots(self)

Returns list of plots.

Return type

List[Plot]

add_plots(self, plots, copy_plots=False)

Add plots to figure.

For every plot a subplot is generated.

Parameters

  • plots (List[Plot]) –

  • copy_plots (bool) –

Return type

None

static from_plots(sid, plots)

Create figure object from list of plots.

Parameters

plots (List[Plot]) –

Return type

Figure

to_dict(self)

Convert to dictionary.

class sbmlsim.plot.Plot(sid, name=None, legend=False, xaxis=None, yaxis=None, curves=None, facecolor=Style.parse_color('white'), title_visible=True)[source]

Bases: BasePlotObject

Plot panel.

A plot is the basic element of a plot. This corresponds to a single panel or axes combination in a plot. Multiple plots create a figure.

Parameters

  • sid (str) –

  • name (str) –

  • legend (bool) –

  • xaxis (Axis) –

  • yaxis (Axis) –

  • curves (List[Curve]) –

__copy__(self)
to_dict(self)

Convert to dictionary.

property figure(self)
Return type

Figure

property experiment(self)
property title(self)
set_title(self, title)
Parameters

title (str) –

property xaxis(self)
Return type

Axis

set_xaxis(self, label, unit=None, **kwargs)

Set axis with all axes attributes.

All argument of Axis are supported.

Parameters

  • label (Union[str, Axis]) –

  • unit (str) –

  • label_visible –

  • kwargs –

Returns

property yaxis(self)
Return type

Axis

set_yaxis(self, label, unit=None, **kwargs)

Set axis with all axes attributes.

All argument of Axis are supported.

Parameters

  • label (Union[str, Axis]) –

  • unit (str) –

  • label_visible –

  • kwargs –

Returns

add_curve(self, curve)

Curves are added via the helper function.

Parameters

curve (Curve) –

property curves(self)
Return type

List[Curve]

curve(self, x, y, xerr=None, yerr=None, single_lines=False, dim_reductions=None, **kwargs)

Adds curve to the plot.

Data can be high-dimensional data from a scan. Additional settings are required which allow to define how things are plotted. E.g. over which dimensions should an error be calculated and which dimensions should be plotted individually.

Parameters
add_data(self, xid, yid, yid_sd=None, yid_se=None, count=None, dataset=None, task=None, label='__yid__', single_lines=False, dim_reduction=None, **kwargs)

Wrapper around plotting.

Parameters

  • xid (str) –

  • yid (str) –

  • count (Union[int, str]) –

  • dataset (str) –

  • task (str) –

  • label (str) –

class sbmlsim.plot.Axis(label=None, unit=None, name=None, scale=AxisScale.LINEAR, min=None, max=None, grid=False, label_visible=True, ticks_visible=True)[source]

Bases: BasePlotObject

Base class for plotting objects.

Parameters

  • label (str) –

  • unit (str) –

  • name (str) –

  • scale (AxisScale) –

  • min (float) –

  • max (float) –

  • grid (bool) –

class AxisScale

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

LINEAR = 1
LOG10 = 2
__copy__(self)
__str__(self)

Return str(self).

property scale(self)
to_dict(self)

Convert to dictionary.

class sbmlsim.plot.SubPlot(plot, row=None, col=None, row_span=1, col_span=1)[source]

Bases: BasePlotObject

A SubPlot is a locate plot in a figure.

Parameters

  • plot (Plot) –

  • row (int) –

  • col (int) –

  • row_span (int) –

  • col_span (int) –

__str__(self)

Return str(self).

class sbmlsim.plot.Curve(x, y, xerr=None, yerr=None, single_lines=False, dim_reductions=None, order=None, style=None, yaxis=None, **kwargs)[source]

Bases: AbstractCurve

Base class for plotting objects.

Parameters
__str__(self)

Return str(self).

static _add_default_style_kwargs(d, dtype)

Default plotting styles

Parameters

  • d (Dict) –

  • dtype (str) –

Return type

Dict

to_dict(self)

Convert to dictionary.

class sbmlsim.plot.ColorType(color)[source]

Bases: object

Parameters

color (str) –

to_dict(self)
__repr__(self)

Return repr(self).

class sbmlsim.plot.MarkerType[source]

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

NONE = 1
SQUARE = 2
CIRCLE = 3
DIAMOND = 4
XCROSS = 5
PLUS = 6
STAR = 7
TRIANGLEUP = 8
TRIANGLEDOWN = 9
TRIANGLELEFT = 10
TRIANGLERIGHT = 11
HDASH = 12
VDASH = 13