tellurium.plotting package¶
Submodules¶
tellurium.plotting.api module¶
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tellurium.plotting.api.
plot
(x, y, show=True, **kwargs)[source]¶ Create a 2D scatter plot.
Parameters: - x – A numpy array describing the X datapoints. Should have the same number of rows as y.
- y – A numpy array describing the Y datapoints. Should have the same number of rows as x.
- tag – A tag so that all traces of the same type are plotted using same color/label (for e.g. multiple stochastic traces).
- tags – Like tag, but for multiple traces.
- name – The name of the trace.
- label – The name of the trace.
- names – Like name, but for multiple traces to appear in the legend.
- labels – The name of the trace.
- alpha – Floating point representing the opacity ranging from 0 (transparent) to 1 (opaque).
- show – show=True (default) shows the plot, use show=False to plot multiple simulations in one plot
- showlegend – Whether to show the legend or not.
- mode – Can be set to ‘markers’ to generate scatter plots, or ‘dash’ for dashed lines.
import numpy as np, tellurium as te result = np.array([[1,2,3,4], [7.2,6.5,8.8,10.5], [9.8, 6.5, 4.3,3.0]]) te.plot(result[:,0], result[:,1], name='Second column', show=False) te.plot(result[:,0], result[:,2], name='Third column', show=False) te.show(reset=False) # does not reset the plot after showing plot te.plot(result[:,0], result[:,3], name='Fourth column', show=False) te.show()
tellurium.plotting.engine module¶
Defines the main classes for plotting which are implemented by the different ploting frameworks, i.e. matplotlib or plotly.
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class
tellurium.plotting.engine.
PlottingEngine
[source]¶ Bases:
object
Abstract parent class of all PlottingEngines.
Helper functions on this class provide methods to create new figures from various datasets.
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accumulateTimecourse
(m, xtitle=None, ytitle=None, title=None, linewidth=2, xlim=None, ylim=None, logx=False, logy=False, xscale='linear', yscale='linear', grid=False, ordinates=None, tag=None, labels=None, figsize=(6, 4), savefig=None, dpi=80, alpha=1.0, **kwargs)[source]¶ Accumulates the traces instead of plotting (like matplotlib with show=False). Call show() to show the plot.
Parameters: m – An array returned by RoadRunner.simulate.
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figureFromTimecourse
(m, ordinates=None, tag=None, alpha=None, title=None, xlim=None, ylim=None, **kwargs)[source]¶ Generate a new figure from a timecourse simulation.
Parameters: m – An array returned by RoadRunner.simulate. Returns: instance of PlottingFigure
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figureFromXY
(x, y, **kwargs)[source]¶ Generate a new figure from x/y data.
Parameters: - x – A column representing x data.
- y – Y data (may be multiple columns).
Returns: instance of PlottingFigure
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newFigure
(title=None, logX=False, logY=False, layout=None, xtitle=None, ytitle=None)[source]¶ Returns PlottingFigure. Needs to be implemented in base class.
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newTiledFigure
(title=None, logX=False, logY=False, layout=None, xtitle=None, ytitle=None)[source]¶ Returns PlottingTiledFigure. Needs to be implemented in base class.
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plot
(x, y, show=True, **kwargs)[source]¶ Plot x & y data.
Parameters: - x – x data.
- y – y data (can be multiple columns).
Returns: instance of PlottingFigure
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plotTimecourse
(m, xtitle=None, ytitle=None, title=None, linewidth=2, xlim=None, ylim=None, logx=False, logy=False, xscale='linear', yscale='linear', grid=False, ordinates=None, tag=None, labels=None, figsize=(6, 4), savefig=None, dpi=80, alpha=1.0, **kwargs)[source]¶ Plots a timecourse from a simulation.
Parameters: m – An array returned by RoadRunner.simulate.
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class
tellurium.plotting.engine.
PlottingFigure
(title=None, layout=<tellurium.plotting.engine.PlottingLayout instance>, logx=False, xtitle=None, logy=False, ytitle=None, selections=None)[source]¶ Bases:
object
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addXYDataset
(x_arr, y_arr, color=None, tag=None, name=None, filter=True, alpha=None, mode=None, logx=None, logy=None, scatter=None, error_y_pos=None, error_y_neg=None, showlegend=None, text=None, dash=None)[source]¶ Adds an X/Y dataset to the plot.
Parameters: - x_arr – A numpy array describing the X datapoints. Should have the same size as y_arr.
- y_arr – A numpy array describing the Y datapoints. Should have the same size as x_arr.
- color – The color to use (not supported by all backends).
- tag – A tag so that all traces of the same type are plotted consistently (for e.g. multiple stochastic traces).
- name – The name of the trace.
- filter – Apply the self.selections filter?
- alpha – Floating point representing the opacity.
- mode – Either ‘lines’ or ‘markers’ (defaults to ‘lines’).
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plot
(x, y, colnames=None, title=None, xtitle=None, logx=None, logy=None, ytitle=None, alpha=None, name=None, names=None, tag=None, tags=None, scatter=None, error_y_pos=None, error_y_neg=None, showlegend=None, label=None, labels=None, text=None, dash=None, color=None)[source]¶ Plot x & y data.
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tellurium.plotting.engine.
filterWithSelections
(self, name, selections)[source]¶ This function is intended to be used as an argument to the filter built-in. It filters out unwanted traces (only those variables specified in selections will be passed through).
Parameters: - name – The symbol we want to potentially filter
- selections – The list of selections we want to plot
tellurium.plotting.engine_mpl module¶
Matplotlib implementation of the plotting engine.
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class
tellurium.plotting.engine_mpl.
MatplotlibEngine
[source]¶ Bases:
tellurium.plotting.engine.PlottingEngine
Matplotlib engine.
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class
tellurium.plotting.engine_mpl.
MatplotlibFigure
(layout=<tellurium.plotting.engine.PlottingLayout instance>, use_legend=True, xtitle=None, ytitle=None, title=None, linewidth=None, xlim=None, ylim=None, logx=None, logy=None, xscale=None, yscale=None, grid=None, ordinates=None, tag=None, labels=None, figsize=(9, 6), savefig=None, dpi=None)[source]¶ Bases:
tellurium.plotting.engine.PlottingFigure
MatplotlibFigure.
tellurium.plotting.engine_null module¶
Plotly implementation of the plotting engine.
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class
tellurium.plotting.engine_null.
NullEngine
[source]¶ Bases:
tellurium.plotting.engine.PlottingEngine
PlottingEngine using plotly.
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class
tellurium.plotting.engine_null.
NullFigure
(title=None, layout=<tellurium.plotting.engine.PlottingLayout instance>, logx=False, logy=False, save_to_pdf=False, xtitle=None, ytitle=None)[source]¶ Bases:
tellurium.plotting.engine.PlottingFigure
PlotlyFigure.
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class
tellurium.plotting.engine_null.
PlotlyLowerTriFigure
(engine, rows, cols)[source]¶ Bases:
tellurium.plotting.engine_null.PlotlyTiledFigure
,tellurium.plotting.engine.LowerTriFigure
tellurium.plotting.engine_plotly module¶
Plotly implementation of the plotting engine.
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class
tellurium.plotting.engine_plotly.
PlotlyEngine
[source]¶ Bases:
tellurium.plotting.engine.PlottingEngine
PlottingEngine using plotly.
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newFigure
(title=None, logX=False, logY=False, layout=<tellurium.plotting.engine.PlottingLayout instance>, xtitle=None, ytitle=None)[source]¶ Returns a figure object.
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class
tellurium.plotting.engine_plotly.
PlotlyFigure
(title=None, layout=<tellurium.plotting.engine.PlottingLayout instance>, logx=False, logy=False, save_to_pdf=False, xtitle=None, ytitle=None)[source]¶ Bases:
tellurium.plotting.engine.PlottingFigure
PlotlyFigure.
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class
tellurium.plotting.engine_plotly.
PlotlyLowerTriFigure
(engine, rows, cols)[source]¶ Bases:
tellurium.plotting.engine_plotly.PlotlyTiledFigure
,tellurium.plotting.engine.LowerTriFigure
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class
tellurium.plotting.engine_plotly.
PlotlyStackedFigure
(title=None, layout=<tellurium.plotting.engine.PlottingLayout instance>, logx=False, logy=False)[source]¶ Bases:
tellurium.plotting.engine_plotly.PlotlyFigure
Stacked figure.
tellurium.plotting.factory module¶
Factory for the engines.