msions.msplot

This module contains functions that are useful for plotting MS data in Python.

Module Contents

Functions

plot_tic(mzml_input[, color, xlabel, ylabel, ...])

Plots TIC against retention time.

plot_ions(mzml_input[, color, xlabel, ylabel, ...])

Plots ions against retention time.
msions.msplot.plot_tic(mzml_input: Union[pandas.DataFrame, str], color: str = '#1f77b4', xlabel: str = 'Time (min)', ylabel: str = 'Total Ion Current', no_labels: bool = False, alpha: float = 1.0, ymax: float = None, fig_params: List[float] = None)[source]

Plots TIC against retention time.

Parameters:

  • mzml_input (pd.DataFrame or str) – The pandas DataFrame containing retention time and TIC or the mzML file.

  • color (str) – The color for the line plot.

  • xlabel (str) – Title for x-axis.

  • ylabel (str) – Title for y-axis.

  • no_labels (bool) – Removes ticks and labels.

  • alpha (float) – Changes the alpha value for the line plot.

  • ymax (float) – Sets the maximum value of the y-axis.

  • fig_params (List[float]) – Sets the figure size and optionally the dpi.

Examples

>>> from msions.msplot import plot_tic
>>> from msions.mzml import tic_df
>>> import matplotlib.pyplot as plot
>>> ms1_df = tic_df("test.mzML")
>>> plot_tic(ms1_df)
>>> plt.show()
msions.msplot.plot_ions(mzml_input: Union[pandas.DataFrame, str], color: str = '#1f77b4', xlabel: str = 'Time (min)', ylabel: str = 'Ions', no_labels: bool = False, alpha: float = 1.0, ymax: float = None, fig_params: List[float] = None)[source]

Plots ions against retention time.

Parameters:

  • mzml_input (pd.DataFrame or str) – The pandas DataFrame containing retention time and TIC or the mzML file.

  • color (str) – The color for the line plot.

  • xlabel (str) – Title for x-axis.

  • ylabel (str) – Title for y-axis.

  • no_labels (bool) – Removes ticks and labels.

  • alpha (float) – Changes the alpha value for the line plot.

  • ymax (float) – Sets the maximum value of the y-axis.

  • fig_params (List[float]) – Sets the figure size and optionally the dpi.

Examples

>>> from msions.msplot import plot_ions
>>> from msions.mzml import tic_df
>>> import matplotlib.pyplot as plot
>>> ms1_df = tic_df("test.mzML")
>>> plot_ions(ms1_df)
>>> plt.show()