mioXpektron.plotting.plot_peaks

Functions

plot_overlapping_peaks(data_dir, ...[, ...])

Overlay spectra with two colors (Cancer vs Control) inferred from file names.

Classes

PlotPeaks([config])	Class for plotting overlapping peaks from multiple spectra files.
PlotPeaksConfig(data_dir[, file_pattern, ...])	Configuration for PlotPeaks class.

class mioXpektron.plotting.plot_peaks.PlotPeaksConfig(data_dir, file_pattern='*.txt', mz_min=0.0, mz_max=1000.0, norm_tic=False, bin_width=0.001, alpha=0.18, show_median=True, show_group_cumulative=True, figsize=(10, 6), cumulative_figsize=(10, 4), color_map=None, save_fig=False, save_path='output_files/plots')

Bases: object

Configuration for PlotPeaks class.

Parameters:

• data_dir (str) – Directory containing spectra files.

• file_pattern (str, default “*.txt”) – Glob pattern for matching spectrum files.

• mz_min (float, default 0.0) – Minimum m/z value for the plotting window.

• mz_max (float, default 1000.0) – Maximum m/z value for the plotting window.

• norm_tic (bool, default False) – If True, normalize intensities by total ion count.

• bin_width (float, default 0.001) – Bin width for interpolation grid.

• alpha (float, default 0.18) – Transparency for individual spectra lines.

• show_median (bool, default True) – If True, overlay median curves on the plot.

• show_group_cumulative (bool, default True) – If True, create cumulative intensity plot.

• figsize (tuple, default (10, 6)) – Figure size for overlay plot.

• cumulative_figsize (tuple, default (10, 4)) – Figure size for cumulative plot.

• color_map (dict, optional) – Dictionary mapping group names to colors.

• save_fig (bool, default False) – If True, save figures as PDF files.

• save_path (str, default "../output_files/plots") – Directory path where PDF files will be saved.

data_dir: str

file_pattern: str = '*.txt'

mz_min: float = 0.0

mz_max: float = 1000.0

norm_tic: bool = False

bin_width: float = 0.001

alpha: float = 0.18

show_median: bool = True

show_group_cumulative: bool = True

figsize: Tuple[int, int] = (10, 6)

cumulative_figsize: Tuple[int, int] = (10, 4)

color_map: Dict[str, str] | None = None

save_fig: bool = False

save_path: str = 'output_files/plots'

class mioXpektron.plotting.plot_peaks.PlotPeaks(config=None)

Bases: object

Class for plotting overlapping peaks from multiple spectra files.

Features: - Load and group spectra by inferred labels (Cancer/Control/Unknown) - Overlay individual spectra with customizable transparency - Plot per-group median curves - Plot cumulative intensity by group - Flexible configuration through PlotPeaksConfig

Example:

>>> config = PlotPeaksConfig(
...     data_dir="data/spectra",
...     mz_min=100.0,
...     mz_max=200.0,
...     norm_tic=True,
...     save_fig=True,
...     save_path="../output_files/plots"
... )
>>> plotter = PlotPeaks(config)
>>> plotter.load_data()
>>> plotter.plot_overlay()
>>> plotter.plot_cumulative()

__init__(config=None)

Initialize PlotPeaks.

Parameters:

config (PlotPeaksConfig, optional) – Configuration object. If None, must set attributes manually.

files: List[str]

grouped_curves: Dict[str, List[Tuple[ndarray, ndarray]]]

set_group_inference(func)

Set custom group inference function.

Parameters:

func (callable) – Function that takes a file path and returns group label.

static load_window(file_path, mz_min, mz_max, norm_tic=False)

Read one spectrum and return (m/z, intensity) in the requested window.

Parameters:

• file_path (str) – Path to a tab or comma-separated spectrum with columns for m/z and intensity. Column names are case-insensitive and support variations: - m/z: “mz”, “m/z”, “M/Z”, “MZ”, “Mz” - intensity: “intensity”, “Intensity”, “INTENSITY”, “int”, “Int”

• mz_min (float) – Inclusive m/z window to extract.

• mz_max (float) – Inclusive m/z window to extract.

• norm_tic (bool, default False) – If True, normalize intensities by total ion count (sum to 1).

Returns:

• mz (np.ndarray)

• inten (np.ndarray) – Intensities scaled by 1e6 (to keep values readable on plots).

Return type:

Tuple[ndarray, ndarray]

load_data()

Load all files matching the pattern and group them by inferred labels.

Raises:

RuntimeError – If no files match the pattern.

Return type:

None

get_group_counts()

Get counts of spectra per group.

Returns:

Dictionary with group names as keys and counts as values.

Return type:

dict

plot_overlay(ax=None, show=True)

Plot overlapping spectra with optional median curves.

Parameters:

• ax (matplotlib.axes.Axes, optional) – Axes to plot on. If None, creates new figure.

• show (bool, default True) – If True, call plt.show() at the end.

Returns:

The figure object.

Return type:

matplotlib.figure.Figure

plot_cumulative(ax=None, show=True)

Plot cumulative intensity curves by group.

Parameters:

• ax (matplotlib.axes.Axes, optional) – Axes to plot on. If None, creates new figure.

• show (bool, default True) – If True, call plt.show() at the end.

Returns:

The figure object.

Return type:

matplotlib.figure.Figure

plot_all()

Convenience method to plot both overlay and cumulative plots.

Returns:

• fig_overlay (matplotlib.figure.Figure) – The overlay plot figure.

• fig_cumulative (matplotlib.figure.Figure) – The cumulative plot figure (or None if disabled).

Return type:

Tuple[Figure, Figure]

Parameters:

config (PlotPeaksConfig | None)

mioXpektron.plotting.plot_peaks.plot_overlapping_peaks(data_dir, file_pattern, mz_min, mz_max, norm_tic=False, alpha=0.18, bin_width=0.001, show_median=True, show_group_cumulative=True)

Overlay spectra with two colors (Cancer vs Control) inferred from file names.

DEPRECATED: This function is maintained for backwards compatibility. Use PlotPeaks class for new code.

Parameters:

• data_dir (str) – Directory containing spectra.

• file_pattern (str) – Glob pattern (e.g., “*.txt”).

• mz_min (float) – m/z window to visualize.

• mz_max (float) – m/z window to visualize.

• norm_tic (bool, default False) – Normalize each spectrum by its TIC prior to plotting.

• alpha (float, default 0.18) – Line transparency for individual spectra.

• bin_width (float, default 0.001) – Common grid step for interpolation (used for medians/cumulative plots).

• show_median (bool, default True) – If True, overlay per-group median curves (thicker lines).

• show_group_cumulative (bool, default True) – If True, plot per-group cumulative intensity curves on a separate figure.

Notes

• Group detection is based on substrings in filenames: “_CC” (Cancer), “_CT” (Control).

• Files without these markers are labeled “Unknown” and plotted in grey.

Examples

>>> # New recommended approach
>>> config = PlotPeaksConfig(
...     data_dir="data/spectra",
...     mz_min=100.0,
...     mz_max=200.0
... )
>>> plotter = PlotPeaks(config)
>>> plotter.load_data()
>>> plotter.plot_all()