Plotting fragmentation output

This module provides functionality to plot the AFprep fragmentation output of a protein.

Functions:

  • plot_domain: Plots a rectangle representing a single protein domain

  • plot_fragment: Plots a rectangle representing a single protein fragment

  • draw_label: Adds a label to the plot

  • calculate_tick_freq: Calculates the frequency of x axis ticks based on sequence length

  • plot_fragmentation_output: Creates and optionally saves a visualization of protein domains and fragments

Dependencies:

  • itertools: Used for cycling through colors for the protein domains.

  • textwrap: Used for wrapping long domain labels.

  • os: Used for creating directories if they do not exist.

  • re: Used for extracting the text part of the domain identifier.

  • matplotlib: Used for plotting the protein domains and fragments.

alphafragment.plot_fragments.calculate_tick_freq(n)

Calculates the frequency of x axis ticks for a given number of residues.

Parameters:

  • n (int): The number of residues in the protein sequence.

Returns:

  • int: The frequency of x-axis ticks.

alphafragment.plot_fragments.draw_label(ax, label, x, x_left, x_right, y, bracket_height, max_x)

Adds a bracket to the plot labeling a specified region with the given text.

Parameters:

  • label (str): The text to be displayed on the bracket.

  • x (float): The x-coordinate of the label.

  • x_left (float): The left x-coordinate of the bracket.

  • x_right (float): The right x-coordinate of the bracket.

  • y (float): The y-coordinate of the bracket.

  • bracket_height (float): The height of the bracket.

  • max_x (float): The maximum x-coordinate allowed for the label to prevent it from spilling out of the plot axes.

  • ax (matplotlib.axes.Axes): The matplotlib axis on which to plot the bracket.

Note:

  • This function adds to the provided axis but does not show it. The display is managed by the caller.

alphafragment.plot_fragments.plot_domain(ax, domain, base_y_position, domain_height, domain_color_cycle, color_mode='origin', type_colors={})

Plots a rectangle representing a single protein domain, on a given matplotlib axis. The color of the domain can be either cycled through a set of predefined colors or set based on domain origin or type.

Parameters:

  • ax (matplotlib.axes.Axes): The matplotlib axis on which to plot the domain.

  • domain (Domain): Expected to be a domain type object.

  • base_y_position (float): The base Y-axis position for the domain rectangle.

  • domain_height (float): The height of the domain rectangle.

  • domain_color_cycle (itertools.cycle): An itertools.cycle object that cycles through a set of colors for the protein domains.

  • color_mode (str): ‘cycle’ for cycling colors, ‘origin’ for color based on domain origin, or ‘type’ for color based on domain identifier.

  • type_colors (dict): A dictionary to store colors for ‘type’ color mode.

Returns:

  • dict: The updated type_colors dictionary, only used if color_mode is ‘type’.

Note:

  • Although this function does have a return, its primary purpose is to add a rectangle to the provided axis. The return is used to maintain color consistency when plotting multiple domains with the ‘type’ color mode.

alphafragment.plot_fragments.plot_fragment(ax, fragment, index, base_y_position, fragment_height, offset)

Plots a rectangle representing a single protein fragment, on a given matplotlib axis. Plots each fragment with a specified vertical offset to prevent overlap between consecutive fragments.

Parameters:

  • ax (matplotlib.axes.Axes): The matplotlib axis on which to plot the fragment.

  • fragment (tuple): A tuple containing fragment start and end positions.

  • index (int): The index of the fragment, used to alternate vertical offset.

  • base_y_position (float): The base Y-axis position for fragment rectangles.

  • fragment_height (float): The height of the fragment rectangle.

  • offset (float): The vertical offset for each fragment (to distinguish between overlapping fragments).

Note:

  • This function adds to the provided axis but does not show it. The display is managed by the caller.

  • Adds 0.5 to either end of the fragment to center it on the residue position.

alphafragment.plot_fragments.plot_fragmentation_output(protein, fragments, save_location=None, figsize=(12, 4), color_mode='type', label=['UniProt', 'manually_defined'])

Creates and optionally saves a visualization of protein domains and fragments. Domains are plotted as colored rectangles, and fragments as red rectangles with a vertical offset so they can be distinguished. The resulting plot can be saved to a file by specifying a save location.

Parameters:

  • protein (Protein): The protein object, expected to have ‘domain_list’ and ‘last_res’ attributes.

  • fragments (list of tuples): A list of tuples, each containing the start and end positions of a fragment.

  • save_location (str, optional): The directory path where the plot image will be saved. If not provided, the image is not saved.

  • figsize (tuple, optional): The size of the output figure.

  • color_mode (‘origin’, ‘cycle’, or ‘type’): Whether to color domains by origin, cycle colors, or type. Defaults to ‘type’.

  • label (list, optional): List of sources for which domains should be labeled. Can include ‘UniProt’, ‘AF’, and ‘manually_defined’. Defaults to labelling UniProt and manually defined domains.

Returns:

  • matplotlib.figure.Figure: The figure object containing the plot.

Note:

  • If save_location is provided and the directory does not exist, it will be created.

  • x-axis represents the protein sequence position, with 1-based indexing.