plotting

Plotting functions for electropherogram analysis

Author: Anja Hess

Date: 2025-AUG-06

Functions

gridplot(df, x, y[, save_dir, title, y_label, ...])

Generate line plot for DNA fragment sizes with masking option for marker peaks

p2stars(p)

Add asterisk based on p-value

stats_plot(path_to_df[, cols_not_to_plot, region_id, ...])

Plot statistical results

peakplot(array, peaks, ladder_id, ref, i, qc_save_dir)

Plot the peaks detected in a DNA size profile

lineplot(df, x, y[, save_dir, title, y_label, ...])

Core line plot function for DNA fragment sizes

ladderplot(df, ladder2type, qc_save_dir[, y_label, ...])

Plot multiple ladders into one plot

Module Contents

plotting.gridplot(df, x, y, save_dir='', title='', y_label='', x_label='', cols_not_to_plot=['bp_pos', 'normalized_fluorescent_units'])

Generate line plot for DNA fragment sizes with masking option for marker peaks

Parameters:

  • df – pandas.DataFrame

  • x – str, the plot’s x variable

  • y – str, the plot’s y variable

  • save_dir – str, path to save the figure

  • title – str, title of the figure

  • y_label – str, y label of the figure

  • x_label – str, x label of the figure

  • cols_not_to_plot – list of columns to exclude from plot to get categorical vars

Returns:

plot is generated and saved to disk.

plotting.p2stars(p)

Add asterisk based on p-value :param p: float, the p-value :return: str

plotting.stats_plot(path_to_df, cols_not_to_plot=None, region_id='region_id', y='value', cut=False)

Plot statistical results :param path_to_df: str :param cols_not_to_plot: list of columns to exclude from plot :return: plots statistics in same directory as input dataframe

plotting.peakplot(array, peaks, ladder_id, ref, i, qc_save_dir, y_label='', x_label='', size_values='')

Plot the peaks detected in a DNA size profile

Parameters:

  • array – np.ndarray

  • peaks – list of int

  • ladder_id – str or int, name of the ladder

  • ref – dtr, type of reference

  • i – int, index of the ladder (potentially multiple)

  • qc_save_dir – str, path to folder to save the figure to

  • y_label – str, y label name

  • x_label – str, x label name

Returns:

plots are generated and saved to disk.

plotting.lineplot(df, x, y, save_dir='', title='', y_label='', x_label='', hue=None, units=None, plot_lower=False, estimator='mean', style=None, window=False)

Core line plot function for DNA fragment sizes

Parameters:

  • df – pandas.DataFrame

  • x – x variable

  • y – y variable

  • save_dir – str, path to save the figure

  • title – str, title of the figure

  • y_label – str, y label of the figure

  • x_label – str, x label of the figure

  • hue – str, optional to set hue parameter

  • units – bool

  • plot_lower – bool

  • estimator – str, which estimator to use

  • style – str, style of line plot

  • window – bool or tuple for x axis limits

Returns:

plots are generated and saved to disk.

plotting.ladderplot(df, ladder2type, qc_save_dir, y_label='', x_label='')

Plot multiple ladders into one plot

Parameters:

  • df – pandas.DataFrame

  • ladder2type – dict

  • qc_save_dir – str

  • y_label – str, y label of the figure

  • x_label – str, x label of the figure

Returns:

plot generated and saved to the QC directory