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#
Parameter |
Type |
Description |
Default |
|---|---|---|---|
x* |
str |
The column name for the X-axis data. Required. |
|
y* |
str |
The column name for the Y-axis data. Required. |
|
by* |
str |
The column name for the grouping variable. |
|
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. |
|
show_plot |
bool |
Whether to display the plot. Defaults to True. |
True |
direction |
Literal[“horizontal”, “vertical”] |
Direction of the line. Defaults to “vertical”. |
“vertical” |
reference_spectrum |
pd.DataFrame | None |
Reference spectrum data. Defaults to None. |
None |
mirror_spectrum |
bool |
Whether to mirror the spectrum. Defaults to False. |
False |
peak_color |
str | None |
Color of the peaks. Defaults to None. |
None |
bin_peaks |
Union[Literal[“auto”], bool] |
Whether to bin peaks. Defaults to False. |
False |
bin_method |
Literal[“none”, “sturges”, “freedman-diaconis”, “mz-tol-bin”] |
Method for binning peaks. Defaults to “mz-tol-bin”. |
“mz-tol-bin” |
num_x_bins |
int |
Number of bins along the X-axis, ignored if bin_peaks is False or “auto”. Defaults to 50. |
50 |
mz_tol |
Union[float, Literal[“freedman-diaconis”, “1pct-diff”]] |
Tolerance for m/z binning. Defaults to “1pct-diff”. |
“1pct-diff” |
annotate_top_n_peaks |
int | None | Literal[“all”] |
Number of top peaks to annotate. Defaults to 5. |
5 |
annotate_mz |
bool |
Whether to annotate m/z values. Defaults to True. |
True |
ion_annotation |
str | None |
Column for ion annotations. Defaults to None. |
None |
sequence_annotation |
str | None |
Column for sequence annotations. Defaults to None. |
None |
custom_annotation |
str | None |
Column for custom annotations. Defaults to None. |
None |
annotation_color |
str | None |
Color for annotations. Defaults to None. |
None |
aggregation_method |
Literal[“mean”, “sum”, “max”] |
Method for aggregating data. Defaults to “max”. |
“max” |
xlabel |
str |
Label for the X-axis. Defaults to “mass-to-charge”. |
“mass-to-charge” |
ylabel |
str |
Label for the Y-axis. Defaults to “Intensity”. |
“Intensity” |
title |
str |
Title of the plot. Defaults to “Mass Spectrum”. |
“Mass Spectrum” |
