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 Core Options

Parameter	Type	Description	Default
kind*	Literal[“chromatogram”, “mobilogram”, “spectrum”, “peakmap”]	Type of plot. Required.
x*	str	The column name for the x-axis data. Required.
y*	str	The column name for the y-axis data. Required.
z*	str	The column name for the z-axis data. Required.
canvas*	Any	Canvas for the plot. For Bokeh, this is a bokeh.plotting.Figure object. For Matplotlib, this is an Axes object, and for Plotly, this is a plotly.graph_objects.Figure object. If none, axis will be created Defaults to None.
height	int	Height of the plot. Defaults to 500.	500
width	int	Width of the plot. Defaults to 500.	500
grid	bool	Whether to show grid. Defaults to True.	True
toolbar_location	str	Location of the toolbar. Defaults to “above”.	“above”
title	str	Title of the plot. Defaults to an empty string.	an empty string
xlabel	str	Label for the X-axis. Defaults to an empty string.	an empty string
ylabel	str	Label for the Y-axis. Defaults to an empty string.	an empty string
zlabel	str	Label for the Z-axis, only applicable if 3D plot. Defaults to an empty string.	an empty string
title_font_size	int	Font size of the title. Defaults to 18.	18
xaxis_label_font_size	int	Font size of the X-axis label. Defaults to 16.	16
yaxis_label_font_size	int	Font size of the Y-axis label. Defaults to 16.	16
zaxis_label_font_size	int	Font size of the Z-axis label. Defaults to 16.	16
xaxis_labelpad	int	Padding for the X-axis label. Defaults to 16.	16
yaxis_labelpad	int	Padding for the Y-axis label. Defaults to 16.	16
zaxis_labelpad	int	Padding for the Z-axis label, only applicable if 3D plot. Defaults to 9.	9
xaxis_tick_font_size	int	Font size for X-axis tick labels. Defaults to 14.	14
yaxis_tick_font_size	int	Font size for Y-axis tick labels. Defaults to 14.	14
zaxis_tick_font_size	int	Font size for Z-axis tick labels. Defaults to 14.	14
y_axis_location	Literal[“left”, “right”]	Location of the Y-axis. Defaults to “left”.	“left”
x_axis_location	Literal[“above”, “below”]	Location of the X-axis. Defaults to “below”.	“below”
annotation_font_size	int	Font size for annotations. Defaults to 12.	12
color	str | Iterator[str]	Color or color iterator for plot elements. Defaults to ColorGenerator.	ColorGenerator
plot_3d	bool	Whether to plot in 3D. Defaults to False.	False
min_border	int	Minimum border size in pixels. Defaults to 0.	0
show_plot	bool	Whether to display the plot. Defaults to True.	True
relative_intensity	bool	Whether to normalize intensity values. Defaults to False.	False
aggregate_duplicates	bool	Whether to aggregate duplicate data points. Defaults to False.	False
legend_config*	LegendConfig | dict	Configuration for the legend, see legend configuration options for more details.
opacity	float	Opacity of plot. Defaults to 1.0.	1.0

Table 2 Legend Options

Parameter	Type	Description	Default
loc	str	Location of the legend. Defaults to “right”.	“right”
orientation	str	Orientation of the legend. Defaults to “vertical”.	“vertical”
title	str	Title of the legend. Defaults to “Legend”.	“Legend”
fontsize	int	Font size of the legend text. Defaults to 10.	10
show	bool	Whether to show the legend. Defaults to True.	True
onClick	Literal[“hide”, “mute”]	Action on legend click. Only valid for Bokeh. Defaults to “mute”.	“mute”
bbox_to_anchor	Tuple[float, float]	Fine control for legend positioning in Matplotlib. Defaults to (1.2, 0.5).	(1.2, 0.5)

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

• Spectrum
• Chromatogram
• Peak Map
• Mobilogram