SpectrumPlot#

class pyopenms_viz._core.SpectrumPlot(data, **kwargs)#

Bases: BaseMSPlot, ABC

__init__(data, **kwargs) → None#
_bin_peaks(df: DataFrame) → DataFrame#

Bin peaks based on x-axis values.

Parameters:

  • data (DataFrame) – The data to bin.

  • x (str) – The column name for the x-axis data.

  • y (str) – The column name for the y-axis data.

Returns:

The binned data.

Return type:

DataFrame

_check_and_aggregate_duplicates()#

Check if duplicate data is present and aggregate if specified. Properly handles data types and only aggregates relevent columns

property _computed_num_bins#

Compute the number of bins based on the number of peaks in the data.

Returns:

The number of bins.

Return type:

int

_get_annotations(data: DataFrame, x: str, y: str)#

Create annotations for each peak. Return lists of texts, x and y locations and colors.

_get_colors(data: DataFrame, kind: Literal['peak', 'annotation'] | None = None)#

Get color generators for peaks or annotations based on config.

_get_ion_color_annotation(ion_annotations: str) → str#

Retrieve the color associated with a specific ion annotation from a predefined colormap.

property _kind#

The kind of plot to assemble. Must be overridden by subclasses.

property _peak_bins#

Get a list of intervals to use in bins. Here bins are not evenly spaced. Currently this only occurs in mz-tol setting

_prepare_data(df, label_suffix='')#

Prepare data for plotting based on configuration (relative intensity, bin peaks)

Parameters:

  • df (DataFrame) – The data to prepare.

  • label_suffix (str, optional) – The suffix to add to the label. Defaults to “”, Only for plotly backend

Returns:

The prepared data.

Return type:

DataFrame

get_spectrum_tooltip_data(spectrum: DataFrame, x: str, y: str)#

Get tooltip data for a spectrum plot.

property known_columns: List[str]#

List of known columns in the data, if there are duplicates outside of these columns they will be grouped in aggregation if specified

load_config(**kwargs)#

Load the configuration settings for the plot.

plot()#

Standard spectrum plot with m/z on x-axis, intensity on y-axis and optional mirror spectrum.