6. Plotting functions¶
Plotting functions for pymzML. The Factory object can hold several plots with several data traces each. The plot will be rendered as interactive plotly plots.
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class
plot.
Factory
(filename=None)¶ Class to plot pymzml.spec.Spectrum as svg/xhtml.
Parameters: filename (str) – Name for the output file. Default = “spectra.xhtml” Example:
>>> import pymzml, get_example_file >>> mzMLFile = 'profile-mass-spectrum.mzml' >>> example_file = get_example_file.open_example(mzMLFile) >>> run = pymzml.run.Run("../mzML_example_files/"+mzMLFile, precisionMSn = 250e-6) >>> p = pymzml.plot.Factory() >>> for spec in run: >>> p.newPlot() >>> p.add(spec.peaks, color=(200,00,00), style='sticks') >>> p.add(spec.centroided_peaks, color=(00,00,00), style='sticks') >>> p.add(spec.reprofiled_peaks, color=(00,255,00), style='sticks') >>> p.save( filename="output/plotAspect.xhtml" , mzRange = (745.2,745.6) )
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newPlot
(header='', mzRange=None, normalize=False, precision='5e-6')¶ Add new plot to the plotting Factory.
Parameters: - header (str) – an optional title that will be printed above the plot
- mzRange (tuple) – Boundaries of the new plot
- normalize (boolean) – whether or not the individal data sets are normalized in the plot
- precision (float) – measuring precision used in handler. Default 5e-6.
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add
(data, color=(0, 0, 0), style='sticks', mzRange=None, opacity=0.8, name=None, plotNum=-1)¶ Add data to the graph.
Parameters: - data (list) – The data added to the graph. Must be list of tuples, like (mz,i) or (mz1, mz2, i, string)
- style (str) –
plotting style. Default = “sticks”.
Currently supported styles are:
- ‘sticks’
- ‘sticks.centroided’
- ‘triangle’ (small, medium or big)
- ‘label.sticks’
- ‘label.triangle’ (small, medium or big)
- ‘label.spline’ (top, medium or bottom)
- ‘label.linear’ (top, medium or bottom)
- color (tuple) – color encoded in RGB. Default = (0,0,0)
- mzRange (tuple) – Boundaries that should be added to the current plot
- opacity (float) – opacity of the data points
- name (str) – name of data in legend
- plotNum (int) – Add data to plot[plotNum]
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info
()¶ Prints summary about the plotting factory, i.e.how many plots and how many datasets per plot.
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save
(filename='spectra.xhtml', xLimits=None)¶ Saves all plots and their data points that have been added to the plotFactory.
Parameters: - filename (str) – Name for the output file. Default = “spectra.xhtml”
- mzRange (tuple) – m/z range which should be considered [start, end]. Default = None
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get_data
()¶ Return data and layout in JSON format.
Returns: JSON compatible python dict Return type: plots (dict)
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