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.

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) )
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.
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]
info()

Prints summary about the plotting factory, i.e.how many plots and how many datasets per plot.

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
get_data()

Return data and layout in JSON format.

Returns:JSON compatible python dict
Return type:plots (dict)