plotting
========

.. py:module:: plotting

.. autoapi-nested-parse::

   Plotting functions for electropherogram analysis


   Author: Anja Hess


   Date: 2025-AUG-06



Functions
---------

.. autoapisummary::

   plotting.gridplot
   plotting.p2stars
   plotting.stats_plot
   plotting.peakplot
   plotting.lineplot
   plotting.ladderplot


Module Contents
---------------

.. py:function:: 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

   :param df: pandas.DataFrame
   :param x: str, the plot's x variable
   :param y: str, the plot's y variable
   :param save_dir: str, path to save the figure
   :param title: str, title of the figure
   :param y_label: str, y label of the figure
   :param x_label: str, x label of the figure
   :param cols_not_to_plot: list of columns to exclude from plot to get categorical vars
   :return: plot is generated and saved to disk.


.. py:function:: p2stars(p)

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


.. py:function:: 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


.. py:function:: 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

   :param array: np.ndarray
   :param peaks: list of int
   :param ladder_id: str or int, name of the ladder
   :param ref: dtr, type of reference
   :param i: int, index of the ladder (potentially multiple)
   :param qc_save_dir: str, path to folder to save the figure to
   :param y_label: str, y label name
   :param x_label: str, x label name
   :return: plots are generated and saved to disk.


.. py:function:: 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

   :param df: pandas.DataFrame
   :param x: x variable
   :param y: y variable
   :param save_dir: str, path to save the figure
   :param title: str, title of the figure
   :param y_label: str, y label of the figure
   :param x_label: str, x label of the figure
   :param hue: str, optional to set hue parameter
   :param units: bool
   :param plot_lower: bool
   :param estimator: str, which estimator to use
   :param style: str, style of line plot
   :param window: bool or tuple for x axis limits
   :return: plots are generated and saved to disk.


.. py:function:: ladderplot(df, ladder2type, qc_save_dir, y_label='', x_label='')

   Plot multiple ladders into one plot

   :param df: pandas.DataFrame
   :param ladder2type: dict
   :param qc_save_dir: str
   :param y_label: str, y label of the figure
   :param x_label: str, x label of the figure
   :return: plot generated and saved to the QC directory