constants
=========

.. py:module:: constants

.. autoapi-nested-parse::

   Constants for electropherogram analysis

   Author: Anja Hess

   Date: 2023-AUG-06



Attributes
----------

.. autoapisummary::

   constants.DISTANCE
   constants.MIN_PEAK_HEIGHT_FACTOR
   constants.MAX_PEAK_WIDTH_FACTOR
   constants.PEAK_PROMINENCE
   constants.INTERPOLATE_FUNCTION
   constants.BACKGROUND_SUBSTRACTION_STATS
   constants.HALO_FACTOR
   constants.ARTIFICIAL_MAX
   constants.ACCEPTED_FORMATS
   constants.LOGFILE_NAME
   constants.YCOL
   constants.XCOL
   constants.YLABEL
   constants.XLABEL
   constants.XLABEL_PRIOR_SIZE
   constants.ALTERNATE_FORMAT
   constants.PALETTE
   constants.LADDER_DICT
   constants.NUC_DICT
   constants.NUC_DICT_250


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

.. py:data:: DISTANCE
   :value: 20


   Minimum required distance of two peaks to be discriminated.


.. py:data:: MIN_PEAK_HEIGHT_FACTOR
   :value: 0.2


   Factor by which to multiply the maximum peak height to set the minimum peak height to be detected. 


.. py:data:: MAX_PEAK_WIDTH_FACTOR
   :value: 1


   Fraction of entire gel length to set the maximum accepted peak width - ONLY FOR THE LADDER, not for sample peaks


.. py:data:: PEAK_PROMINENCE
   :value: (0.2, None)


   Tuple, minimum peak prominence 


.. py:data:: INTERPOLATE_FUNCTION
   :value: 'linear'


   Function to interpolate missing base pair values based on user-annotated values 


.. py:data:: BACKGROUND_SUBSTRACTION_STATS
   :value: 0.1


.. py:data:: HALO_FACTOR
   :value: 0


.. py:data:: ARTIFICIAL_MAX
   :value: 100000


.. py:data:: ACCEPTED_FORMATS
   :value: ['.csv', '.png', '.jpeg', '.jpg']


   Possible input formats


.. py:data:: LOGFILE_NAME
   :value: 'dnavi.log'


.. py:data:: YCOL
   :value: 'normalized_fluorescent_units'


   Standardized y axis name


.. py:data:: XCOL
   :value: 'bp_pos'


   Standardized x axis name


.. py:data:: YLABEL
   :value: 'Sample Intensity [Normalized FU]'


   Standardized y labe name


.. py:data:: XLABEL
   :value: 'Size [bp]'


   Standardized x label name


.. py:data:: XLABEL_PRIOR_SIZE
   :value: 'Size'


   Standardized x label name before interpolation


.. py:data:: ALTERNATE_FORMAT
   :value: 'svg'


   The second format apart from .pdf to save images to


.. py:data:: PALETTE
   :value: ['cadetblue', '#fbc27b', '#d56763', 'darkgrey', '#a7c6c9', '#2d435b', '#d56763', 'darkred',...


   Standardized color palette


.. py:data:: LADDER_DICT

   Dictionary with standardized peak size options (beta)


.. py:data:: NUC_DICT

.. py:data:: NUC_DICT_250

   Dictionary with standardized peak size options (beta)