Parameters

Pyopenms-viz plotting occurs by calling the .plot() method on a pandas dataframe. Mandatory values are the column names for the x, y (and possibly z) axis as well as the kind of plot. Additional options are listed below.

General Options include (mandatory fields are starred)

Table 1 General Options

Parameter	Default	Type	Description
x*		str	The column name for x-axis data
y*		str	The column name for y-axis data
kind*		str	‘The kind of plot to create. One of: [ “line”, “vline”, scatter”, “chromatogram”, “mobilogram”, “spectrum”, “peak_map”]
by		str	The column name to group by
backend		str	‘Backend to use. One of: [ “ms_matplotlib”, “ms_bokeh”, “ms_plotly” ]. Must be specified if not set globally
relative_intensity	False	bool	Convert y-axis values to relative intensity
height		int	Height of plot, units dependent on backend.
width		int	Width of plot in pixels, units dependent on backend.
grid	False	bool	Whether to show grid on the plot
toolbar_location	“above”		Location of toolbar for interactive plots. One of: [“above”, “below”, “left”]
fig	None	fig	Existing Figure object to plot on
xlabel	None	str	Label for x axis
ylabel	None	str	Label for y axis
show_plot	True	bool	Whether to display the plot. If plot is not shown, will return the plot object corresponding with the backend. If plot is displayed the method returns None

Please click on a kind of plot below for more details on their specific parameters:

• Spectrum
• Chromatogram
• Peak Map
• Mobilogram