Spectrum#

A spectrum can be plot using kind = “spectrum”. In this plot, mass-to-charge ratio is on the x-axis and intensity is on the y-axis.

Parameters#

Table 2 Chromatogram Options#
Parameter	Default	Type	Description
x*		str	The column name for x-axis data
y*		str	The column name for y-axis data
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
reference_spectrum		DataFrame	alternative dataframe to plot as the reference spectrum.
mirror_spectrum	False	bool	Whether to plot a mirror spectrum
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
bin_peaks	False	bool \| “auto”	If True, will bin peaks based on specified number of bins in num_x_bins. If “auto”, will automatically determine the number of bins based on the data using the strategy specified in bin_method.
bin_method		“mz-tol-bin”	Binning method, one of [ “none”, “sturges”, “freedman-diaconis”, “mz-tol-bin”]
num_x_bins	50	int	Number of bins, will be adjusted if bin_peaks is “auto”
aggregation_method		“mean	How to aggregate duplicate dataframe entries, one of [ “mean”, “sum”, “max” ]
mz_tol	“1pct-diff”		mass-to-charge tolerance for “mz_tol_bin” bin_method. Can be one of [float, ‘freedman-diaconis’, ‘1pct-diff’]
peak_color	None	None \| str	Peak color for the plot. If not specified will be automatically generated. Overridden by annotation_color. E.g. if a color is specified in the annotation_color column than this will be overridden.
annotate_top_n_peaks	5	int	Number of peaks to annotate
annotate_mz	True	bool	whether to annotate the top n peaks with their mz values
sequence_annotation		str	column containing sequence_annotation information.
custom_annotation		str	column containing custom annotation
annotation_color		str	column containing the annotation color. If not specified will be automatically generated