`sbmlsim.plot.plotting`¶

Base classes for storing plotting information.

The general workflow of generating plotting information is the following.

Within simulation experiments abstract plotting information is stored.
i.e., how from the data plots can be generated.

Module Contents¶

Classes¶

`BasePlotObject`	Base class for plotting objects.
`LineType`	Generic enumeration.
`MarkerType`	Generic enumeration.
`CurveType`	Generic enumeration.
`ColorType`
`Line`
`Marker`
`Fill`
`Style`	Base class for plotting objects.
`Axis`	Base class for plotting objects.
`AbstractCurve`	Base class for plotting objects.
`Curve`	Base class for plotting objects.
`Plot`	Plot panel.
`SubPlot`	A SubPlot is a locate plot in a figure.
`Figure`	A figure consists of multiple subplots.

Attributes¶

`logger`
`DEFAULT_COLORS`

sbmlsim.plot.plotting.logger[source]¶

sbmlsim.plot.plotting.DEFAULT_COLORS = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f',...[source]¶

class sbmlsim.plot.plotting.BasePlotObject(sid, name)[source]¶

Bases: object

Base class for plotting objects.

Parameters

sid (str) –
name (str) –

class sbmlsim.plot.plotting.LineType[source]¶

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

NONE = 1[source]¶

SOLID = 2[source]¶

DASH = 3[source]¶

DOT = 4[source]¶

DASHDOT = 5[source]¶

DASHDOTDOT = 6[source]¶

class sbmlsim.plot.plotting.MarkerType[source]¶

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

NONE = 1[source]¶

SQUARE = 2[source]¶

CIRCLE = 3[source]¶

DIAMOND = 4[source]¶

XCROSS = 5[source]¶

PLUS = 6[source]¶

STAR = 7[source]¶

TRIANGLEUP = 8[source]¶

TRIANGLEDOWN = 9[source]¶

TRIANGLELEFT = 10[source]¶

TRIANGLERIGHT = 11[source]¶

HDASH = 12[source]¶

VDASH = 13[source]¶

class sbmlsim.plot.plotting.CurveType[source]¶

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

POINTS = 1[source]¶

BAR = 2[source]¶

BARSTACKED = 3[source]¶

HORIZONTALBAR = 4[source]¶

HORIZONTALBARSTACKED = 5[source]¶

POLARPOINT = 6[source]¶

POLARBAR = 7[source]¶

POLARBARSTACKED = 8[source]¶

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

Bases: object

Parameters: color (str) –

to_dict(self)[source]¶

__repr__(self)[source]¶: Return repr(self).

class sbmlsim.plot.plotting.Line[source]¶

Bases: object

type :LineType[source]¶

color :ColorType[source]¶

thickness :float[source]¶

to_dict(self)[source]¶

class sbmlsim.plot.plotting.Marker[source]¶

Bases: object

size :float[source]¶

type :MarkerType[source]¶

fill :ColorType[source]¶

line_color :ColorType[source]¶

line_thickness :float = 1.0[source]¶

to_dict(self)[source]¶

class sbmlsim.plot.plotting.Fill[source]¶

Bases: object

color :ColorType[source]¶

second_color :ColorType[source]¶

class sbmlsim.plot.plotting.Style(sid=None, name=None, base_style=None, line=None, marker=None, fill=None)[source]¶

Bases: BasePlotObject

Base class for plotting objects.

Parameters

sid (str) –
name (str) –
base_style (Style) –
line (Line) –
marker (Marker) –
fill (Fill) –

MPL2SEDML_LINESTYLE_MAPPING[source]¶

SEDML2MPL_LINESTYLE_MAPPING[source]¶

MPL2SEDML_MARKER_MAPPING[source]¶

SEDML2MPL_MARKER_MAPPING[source]¶

to_mpl_kwargs(self)[source]¶

Convert to matplotlib plotting arguments

Return type: Dict

static parse_color(color, alpha=1.0)[source]¶

Parse given color and add alpha information.

Parameters

color (str) –
alpha (float) –

Returns

ColorType or None

Return type

Optional[ColorType]

static from_mpl_kwargs(**kwargs)[source]¶

Creates style from matplotlib arguments.

Parameters

alpha – alpha setting
color – color setting
kwargs –

Returns

Return type

Style

class sbmlsim.plot.plotting.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[source]¶

Bases: enum.Enum

Generic enumeration.

Derive from this class to define new enumerations.

LINEAR = 1[source]¶

LOG10 = 2[source]¶

__copy__(self)[source]¶

__str__(self)[source]¶: Return str(self).

property scale(self)[source]¶

to_dict(self)[source]¶: Convert to dictionary.

class sbmlsim.plot.plotting.AbstractCurve(sid, name, x, order, style, yaxis)[source]¶

Bases: BasePlotObject

Base class for plotting objects.

Parameters

sid (str) –
name (str) –
x (sbmlsim.data.Data) –
order (int) –
style (Style) –
yaxis (Axis) –

class sbmlsim.plot.plotting.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

x (sbmlsim.data.Data) –
y (sbmlsim.data.Data) –
xerr (sbmlsim.data.Data) –
yerr (sbmlsim.data.Data) –
single_lines (bool) –
dim_reductions (List[str]) –
style (Style) –

__str__(self)[source]¶: Return str(self).

static _add_default_style_kwargs(d, dtype)[source]¶

Default plotting styles

Parameters

d (Dict) –
dtype (str) –

Return type

Dict

to_dict(self)[source]¶: Convert to dictionary.

class sbmlsim.plot.plotting.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)[source]¶

to_dict(self)[source]¶: Convert to dictionary.

property figure(self)[source]¶

Return type: Figure

property experiment(self)[source]¶

property title(self)[source]¶

set_title(self, title)[source]¶

Parameters: title (str) –

property xaxis(self)[source]¶

Return type: Axis

set_xaxis(self, label, unit=None, **kwargs)[source]¶

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)[source]¶

Return type: Axis

set_yaxis(self, label, unit=None, **kwargs)[source]¶

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)[source]¶

Curves are added via the helper function.

Parameters: curve (Curve) –

property curves(self)[source]¶

Return type: List[Curve]

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

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

x (sbmlsim.data.Data) –
y (sbmlsim.data.Data) –
xerr (sbmlsim.data.Data) –
yerr (sbmlsim.data.Data) –
single_lines (bool) –
dim_reductions (List[str]) –

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)[source]¶

Wrapper around plotting.

Parameters

xid (str) –
yid (str) –
count (Union[int, str]) –
dataset (str) –
task (str) –
label (str) –

class sbmlsim.plot.plotting.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)[source]¶: Return str(self).

class sbmlsim.plot.plotting.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[source]¶

fig_facecolor = white[source]¶

fig_subplots_wspace = 0.3[source]¶

fig_subplots_hspace = 0.3[source]¶

panel_width = 7[source]¶

panel_height = 5[source]¶

fig_titlesize = 25[source]¶

fig_titleweight = bold[source]¶

axes_titlesize = 20[source]¶

axes_titleweight = bold[source]¶

axes_labelsize = 18[source]¶

axes_labelweight = bold[source]¶

xtick_labelsize = 15[source]¶

ytick_labelsize = 15[source]¶

legend_fontsize = 13[source]¶

legend_loc = best[source]¶

_area_interpolation_points = 300[source]¶

num_subplots(self)[source]¶: Number of existing subplots.

num_panels(self)[source]¶: Number of available spots for plots.

set_title(self, title)[source]¶

create_plots(self, xaxis=None, yaxis=None, legend=True)[source]¶

Template function for creating plots

Parameters

xaxis (Axis) –
yaxis (Axis) –
legend (bool) –

Return type

List[Plot]

property plots(self)[source]¶

get_plots(self)[source]¶

Returns list of plots.

Return type: List[Plot]

add_plots(self, plots, copy_plots=False)[source]¶

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)[source]¶

Create figure object from list of plots.

Parameters: plots (List[Plot]) –
Return type: Figure

to_dict(self)[source]¶: Convert to dictionary.

sbmlsim.plot.plotting¶

Module Contents¶

Classes¶

Attributes¶

`sbmlsim.plot.plotting`¶