prolint.plotting.residues
=========================

.. py:module:: prolint.plotting.residues

.. autoapi-nested-parse::

   Residue metrics plotters for per-residue visualization.

   This module provides bar charts and logo grids for displaying
   per-residue contact metrics.



Classes
-------

.. autoapisummary::

   prolint.plotting.residues.ResidueMetricsPlotter
   prolint.plotting.residues.LogoGridPlotter


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

.. py:class:: ResidueMetricsPlotter

   Bases: :py:obj:`prolint.plotting.base.BasePlotter`


   Plotter for per-residue contact metrics.

   Visualizes metrics as bar charts or scatter plots with
   amino acid coloring and highlighting options.

   .. seealso::

      :py:obj:`MetricsAnalysis`
          Generates per-residue metric data
      
      :py:obj:`LogoGridPlotter`
          Grid-based residue visualization


   .. py:attribute:: name
      :value: 'residue_metrics'



   .. py:attribute:: required_analysis
      :value: 'metrics'



   .. py:attribute:: description
      :value: 'Per-residue metrics visualization (bar/scatter)'



   .. py:method:: validate_result(result: prolint.analysis.base.AnalysisResult) -> None
      :classmethod:


      Validate that result contains residue metrics data.



   .. py:method:: plot(result: prolint.analysis.base.AnalysisResult, style: str = 'bar', colorscheme: str = 'prolint', xlabel: str = 'Residue', ylabel: str = 'Value', title: str = 'Per-Residue Metrics', figsize: Optional[Tuple[float, float]] = None, ax: Optional[matplotlib.axes.Axes] = None, show_aa_labels: bool = True, highlight_residues: Optional[List[int]] = None, bar_width: float = 0.8, sort_by_value: bool = False, marker_size: int = 50) -> Tuple[matplotlib.figure.Figure, matplotlib.axes.Axes]
      :classmethod:


      Create per-residue metrics visualization.

      :param result: Result from metrics analysis.
      :type result: AnalysisResult
      :param style: Plot style.
      :type style: {"bar", "scatter"}, default="bar"
      :param colorscheme: Color scheme ("prolint", "amino_acid", or scale name).
      :type colorscheme: str, default="prolint"
      :param show_aa_labels: Whether to show amino acid labels on x-axis.
      :type show_aa_labels: bool, default=True
      :param highlight_residues: Residue IDs to highlight.
      :type highlight_residues: list of int, optional
      :param sort_by_value: Whether to sort residues by value.
      :type sort_by_value: bool, default=False
      :param ax: Existing axes to plot on.
      :type ax: Axes, optional

      :returns: Matplotlib figure and axes objects.
      :rtype: tuple of (Figure, Axes)



.. py:class:: LogoGridPlotter

   Bases: :py:obj:`prolint.plotting.base.BasePlotter`


   Plotter for grid-based residue logo visualization.

   Displays residues as colored cells arranged in rows with
   one-letter amino acid codes and residue numbers.

   .. seealso::

      :py:obj:`MetricsAnalysis`
          Generates per-residue metric data
      
      :py:obj:`ResidueMetricsPlotter`
          Bar/scatter visualization


   .. py:attribute:: name
      :value: 'logo_grid'



   .. py:attribute:: required_analysis
      :value: 'metrics'



   .. py:attribute:: description
      :value: 'Grid-based residue logo plot with amino acid annotations'



   .. py:method:: validate_result(result: prolint.analysis.base.AnalysisResult) -> None
      :classmethod:


      Validate that result contains residue metrics data.



   .. py:method:: plot(result: prolint.analysis.base.AnalysisResult, colorscheme: str = 'prolint', residues_per_row: int = 80, cell_size: float = 0.3, title: str = 'Residue Logo Plot', figsize: Optional[Tuple[float, float]] = None, highlight_residues: Optional[List[int]] = None) -> Tuple[matplotlib.figure.Figure, matplotlib.axes.Axes]
      :classmethod:


      Create grid-based residue logo visualization.

      :param result: Result from metrics analysis.
      :type result: AnalysisResult
      :param colorscheme: Color scale name for value-based coloring.
      :type colorscheme: str, default="prolint"
      :param residues_per_row: Number of residue cells per row.
      :type residues_per_row: int, default=80
      :param cell_size: Size of each cell in inches.
      :type cell_size: float, default=0.3
      :param title: Plot title.
      :type title: str, default="Residue Logo Plot"
      :param figsize: Figure dimensions (width, height). Auto-calculated if None.
      :type figsize: tuple of (float, float), optional
      :param highlight_residues: Residue IDs to highlight with colored borders.
      :type highlight_residues: list of int, optional

      :returns: Matplotlib figure and axes objects.
      :rtype: tuple of (Figure, Axes)