agglovar.kmer.plot
==================

.. py:module:: agglovar.kmer.plot

.. autoapi-nested-parse::

   Routines for generating dotplots.



Functions
---------

.. autoapisummary::

   agglovar.kmer.plot.dotplot


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

.. py:function:: dotplot(seq_x: str, seq_y: str, config: dict = None, title: str = None, anno_list: list[dict] = None) -> t_mpl_Figure

   Generate a dotplot for two sequences.

   Configuration items:

   * label_x, label_y: Axis labels (default "Sequence", and "Reference")
   * start_x, start_y: Start position along each axis. Should be the first base position in the
     extracted region (Default 0).
   * linewidth: Width of the lines (default 1)
   * plot_width, plot_height, plot_dpi: Plot dimensions (default 7, 7, 300)
   * invert_y: Invert the y axis (default False)
   * color: A tuple of matplotlib colors for forward and reverse k-mer dots (default ("black", "red"))
     * May be "reverse" or "rev" to reverse the order of the default colors.
   * color_reverse: Reverse the order of the default colors (defaults to invert_y)
   * kmer_util: A kmer_util.KmerUtil object (default None)
   * k: K-mer size if kmer_util is missing (default 32)

   :params seq_x: Sequence 1 (horizontal axis).
   :params seq_y: Sequence 2 (vertical axis).
   :params config: Configuration dictionary.
   :params title: Figure title.
   :params anno_list: List of annotations.

   :returns: A matplotlib figure.

   :raises ImportError: If matplotlib is not installed.
   :raises ValueError: If an invalid value is provided for an argument.
   :raises KeyError: If `anno_list` contains annotation definitions that are missing required elements.`