biotite 0.41.1__cp312-cp312-macosx_10_16_arm64.whl

biotite/sequence/graphics/features.py

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+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.sequence.graphics"
+__author__ = "Patrick Kunzmann"
+__all__ = ["plot_feature_map", "FeaturePlotter", "MiscFeaturePlotter",
+           "CodingPlotter", "PromoterPlotter", "TerminatorPlotter",
+           "RBSPlotter"]
+
+import copy
+import abc
+import numpy as np
+from ...visualize import colors, AdaptiveFancyArrow
+from ..annotation import Annotation, Feature, Location
+
+
+def plot_feature_map(axes, annotation, loc_range=None,
+                     multi_line=True, symbols_per_line=1000,
+                     show_numbers=False, number_size=None, line_width=0.05,
+                     show_line_position=False, spacing=0.25,
+                     feature_plotters=None, style_param=None):
+    """
+    Plot a sequence annotation, by showing the range of each feature
+    on one or multiple position depicting line(s).
+
+    This function uses :class:`FeaturePlotter` objects to draw the
+    features.
+    This function internally uses a list of plotters, where the
+    first plotter in the list, that supports a feature, is used to draw
+    that feature.
+    The amount of features that can be visualized by default is limited.
+    Features, that are not supported otherwise, are visualized as simple
+    rectangles.
+    Additional :class:`FeaturePlotter` objects, that are supplied in the
+    `feature_plotters` parameters, can be used to add support for
+    further features or to customize the appearance of certain features.
+
+    Parameters
+    ----------
+    axes : Axes
+        A *Matplotlib* axes, that is used as plotting area.
+    annotation : Annotation
+        The annotation to be visualized.
+    loc_range : tuple (int, int), optional
+        The start and exclusive stop location that is visualized.
+        By default, the location range starts from the first
+        base/residue and ends at the last base/residue of all features,
+        ensuring that the entire annotation is drawn.
+    multi_line : bool, optional
+        If true, the annotation is segmented into multiple lines with a
+        line break all `symbols_per_line` lines.
+        Otherwise, the entire location range is put into a single line.
+    symbols_per_line : int, optional
+        The amount of
+        Does not have an effect, if `multi_line` is false.
+    show_numbers : bool, optional
+        If true, the sequence position the base/residue of a line is
+        shown on the right side of the plot.
+    number_size : float, optional
+        The font size of the position numbers
+    line_width : float, optional
+        The size of the continuous line as fraction of the height of
+        the drawn features.
+    show_line_position : bool, optional
+        If true the position within a line is plotted.
+    spacing : float, optional
+        The size of the spacing between the lines as fraction of the
+        height of the drawn features.
+    feature_plotters : list of FeaturePlotter, optional
+        Custom plotters for features.
+        The list is iterated from the beginning until a
+        :class:`FeaturePlotter` matches the respective feature
+        (`FeaturePlotter.matches()` returns `True`).
+        This :class:`FeaturePlotter` is then used to draw the feature.
+        Therefore, the :class:`FeaturePlotter` instances in the list
+        have descending priority.
+        The default plotters are appended after this supplied list,
+        i.e. the default plotters have a lower priority.
+    style_param : dict
+        Additional style parameters that are given to the
+        :class:`FeaturePlotter` objects.
+
+    Notes
+    -----
+    Good visulation results are obtained only for non-overlapping
+    features.
+    When two features overlap, their drawing area does also overlap.
+    """
+    from matplotlib.transforms import Bbox
+    from matplotlib.patches import Rectangle
+
+    if loc_range is None:
+        loc_range = annotation.get_location_range()
+    loc_range_length = loc_range[1] - loc_range[0]
+    if multi_line:
+        symbols_per_line = symbols_per_line
+    else:
+        # Line length covers the entire location range
+        symbols_per_line = loc_range_length
+    
+    plotters = [
+        PromoterPlotter(),
+        TerminatorPlotter(),
+        RBSPlotter(),
+        CodingPlotter(),
+        MiscFeaturePlotter()
+    ]
+    if feature_plotters is not None:
+        plotters = list(feature_plotters) + plotters
+
+    style_param = {} if style_param is None else style_param
+
+    line_count = loc_range_length // symbols_per_line
+    # Only extend line count by 1 if there is a remainder
+    if loc_range_length % symbols_per_line != 0:
+        line_count += 1
+
+
+    ### Draw lines ###
+    remaining_symbols = loc_range_length
+    y = 0.5
+    while remaining_symbols > 0:
+        if remaining_symbols > symbols_per_line:
+            # Line spans the entire plot (horizontally)
+            line_length = symbols_per_line
+        else:
+            # Last line -> Line spans to end of annotation
+            line_length = remaining_symbols
+        axes.add_patch(Rectangle(
+            (0, y-line_width/2), line_length, line_width,
+            color="gray", linewidth=0
+        ))
+        # Increment by spacing and width (=1) of feature
+        y += spacing + 1
+        remaining_symbols -= symbols_per_line
+    
+    ### Draw features ###
+    line_start_loc = loc_range[0]
+    y = 0
+    while line_start_loc < loc_range[1]:
+        annotation_for_line = annotation[
+            line_start_loc : line_start_loc + symbols_per_line
+        ]
+        for feature in annotation_for_line:
+            plotter = None
+            # Identify fitting plotter
+            for potentail_plotter in plotters:
+                if potentail_plotter.matches(feature):
+                    # Take first fitting plotter in list
+                    plotter = potentail_plotter
+                    break
+            if plotter is not None:
+                for loc in feature.locs:
+                    loc_len = loc.last - loc.first + 1
+                    # Get start location realtive to start if line
+                    loc_in_line = loc.first - line_start_loc
+                    x = loc_in_line
+                    # Line width multiplied by percentage of line
+                    width = loc_len
+                    height = 1
+                    bbox = Bbox.from_bounds(x, y, width, height)
+                    plotter.draw(
+                        axes, feature, bbox, loc,
+                        style_param=style_param
+                    )
+        # Increment by spacing and width (=1) of feature
+        y += spacing + 1
+        remaining_symbols += symbols_per_line
+        line_start_loc += symbols_per_line
+    
+    ### Draw position numbers  ###
+    ticks = []
+    tick_labels = []
+    if show_numbers:
+        # Numbers at center height of each feature line -> 0.5
+        y = 0.5
+        for i in range(line_count):
+            if i == line_count-1:
+                # Last line -> get number of last column in trace
+                loc = loc_range[1] -1
+            else:
+                loc = loc_range[0] + ((i+1) * symbols_per_line) -1
+            ticks.append(y)
+            tick_labels.append(str(loc))
+            # Increment by spacing and width of feature (1)
+            y += spacing + 1
+    axes.set_yticks(ticks)
+    axes.set_yticklabels(tick_labels)
+
+
+    axes.set_xlim(0, symbols_per_line)
+    # Y-axis starts from top
+    axes.set_ylim(1*line_count + spacing*(line_count-1), 0)
+    axes.set_frame_on(False)
+    # Draw location numbers on right side
+    axes.get_yaxis().set_tick_params(
+        left=False, right=False, labelleft=False, labelright=True
+    )
+    # Remove ticks and set number font size
+    axes.yaxis.set_tick_params(
+        left=False, right=False, labelsize=number_size
+    )
+    
+    if show_line_position:
+        axes.xaxis.set_tick_params(
+            top=False, bottom=True, labeltop=False, labelbottom=True
+        )
+    else:
+        axes.xaxis.set_tick_params(
+            top=False, bottom=False, labeltop=False, labelbottom=False
+        )
+
+
+class FeaturePlotter(metaclass=abc.ABCMeta):
+    """
+    A :class:`FeaturePlotter` is an object, that 'knows' how to draw a
+    certain type of sequence feature onto a :class:`matplotlib.Axes`.
+
+    Whether the :class:`FeaturePlotter` is able to draw a feature, is
+    checked via the :func:`matches()` method.
+    The visualization of a compatible feature is conducted in the
+    :func:`draw()` method.
+    """
+
+    def __init__(self):
+        pass
+
+    @abc.abstractmethod
+    def matches(self, feature):
+        """
+        Check, whether this object is able to draw a given sequence
+        feature.
+
+        Parameters
+        ----------
+        feature : Feature
+            The sequence feature to be checked.
+        
+        Returns
+        -------
+        compatibility : bool
+            True, if this object is able to draw the given `feature`,
+            false otherwise.
+        """
+        pass
+    
+    @abc.abstractmethod
+    def draw(self, axes, feature, bbox, location, style_param):
+        """
+        Draw a feature onto an axes.
+
+        Parameters
+        ----------
+        axes : Axes
+            A *Matplotlib* axes, that is used as plotting area.
+        feature : Feature
+            The feature to be drawn.
+        bbox : Bbox
+            The bounding box, that describes the area on the `axes`,
+            where the feature should be drawn.
+        location : int
+            The location of the feature, that should be drawn.
+            Might be useful, when the visualization is dependent
+            on e.g. location defects.
+        style_param : dict
+            Additional style parameters.
+        """
+        pass
+
+
+class CodingPlotter(FeaturePlotter):
+    """
+    A plotter for the *CDS* and *gene* features.
+
+    Draws an arrow with a 90 degrees tip.
+
+    Parameters
+    ----------
+    tail_width : float, optional
+        The width of the arrow tail
+        as fraction of the feature drawing area height.
+    head_width : float, optional
+        The width of the arrow head
+        as fraction of the feature drawing area height.
+    """
+    
+    def __init__(self, tail_width=0.5, head_width=0.8):
+        self._tail_width = tail_width
+        self._head_width = head_width
+
+    def matches(self, feature):
+        if feature.key in ["CDS", "gene"]:
+            return True
+        else:
+            return False
+        
+    def draw(self, axes, feature, bbox, loc, style_param):
+        y = bbox.y0 + bbox.height/2
+        dy = 0
+        if loc.strand == Location.Strand.FORWARD:
+            x = bbox.x0
+            dx = bbox.width
+        else:
+            x = bbox.x1
+            dx = -bbox.width
+        
+        if  (
+                loc.strand == Location.Strand.FORWARD 
+                and loc.defect & Location.Defect.MISS_RIGHT
+            ) or (
+                loc.strand == Location.Strand.REVERSE 
+                and loc.defect & Location.Defect.MISS_LEFT
+            ):
+                # If the feature extends into the prevoius or next line
+                # do not draw an arrow head
+                draw_head = False
+        else:
+                draw_head = True
+        
+        # Create head with 90 degrees tip -> head width/length ratio = 1/2
+        axes.add_patch(AdaptiveFancyArrow(
+            x, y, dx, dy, self._tail_width, self._head_width, head_ratio=0.5,
+            draw_head=draw_head, color=colors["dimgreen"], linewidth=0
+        ))
+
+        if feature.key == "CDS":
+            if "product" not in feature.qual:
+                label = None
+            elif feature.qual["product"] == "hypothetical protein":
+                label = None
+            else:
+                label = feature.qual["product"]
+        elif feature.key == "gene":
+            if  "gene" not in feature.qual:
+                label = None
+            else:
+                label = feature.qual["gene"]
+        
+        if label is not None:
+            center_x = bbox.x0 + bbox.width/2
+            center_y = bbox.y0 + bbox.height/2
+            axes.text(
+                center_x, center_y, label, color="black",
+                ha="center", va="center", size=11)
+
+
+class MiscFeaturePlotter(FeaturePlotter):
+    """
+    A plotter that matches any feature.
+
+    Draws a simple Rectangle.
+
+    Parameters
+    ----------
+    height : float, optional
+        The width of the rectangle
+        as fraction of the feature drawing area height.
+    """
+
+    def __init__(self, height=0.4):
+        self._height = height
+
+    def matches(self, feature):
+        return True
+        
+    def draw(self, axes, feature, bbox, loc, style_param):
+        from matplotlib.patches import Rectangle
+
+        rect = Rectangle(
+            (bbox.x0, bbox.y0 + bbox.height/2 * (1-self._height)),
+            bbox.width, bbox.height*self._height,
+            color=colors["dimorange"], linewidth=0
+        )
+        axes.add_patch(rect)
+
+class PromoterPlotter(FeaturePlotter):
+    """
+    A plotter for *regulatory* features with the *promoter* or
+    *TATA_box* class.
+
+    Draws a simple curved thin black arrow.
+
+    Parameters
+    ----------
+    line_width : float, optional
+        The width of the curved arrow tail.
+    head_width : float, optional
+        The width of the arrow head
+    head_length : float, optional
+        The length of the arrow.
+    head_height : float, optional
+        The Y-position of the arrow head
+        as fraction of the halffeature drawing area height.
+    """
+
+    def __init__(self, line_width=2, head_width=2,
+                 head_length=6, head_height=0.8):
+        self._line_width = line_width
+        self._head_width = head_width
+        self._head_length = head_length
+        self._head_height = head_height
+
+    def matches(self, feature):
+        if feature.key == "regulatory":
+            if "regulatory_class" in feature.qual:
+                if feature.qual["regulatory_class"] in ["promoter","TATA_box"]:
+                    return True
+        return False
+        
+    def draw(self, axes, feature, bbox, loc, style_param):
+        from matplotlib.patches import FancyArrowPatch, ArrowStyle
+        from matplotlib.path import Path
+
+        x_center = bbox.x0 + bbox.width/2
+        y_center = bbox.y0 + bbox.height/2
+
+        path = Path(
+            vertices=[
+                (bbox.x0, y_center),
+                (bbox.x0, y_center - bbox.height/2 * self._head_height),
+                (bbox.x1, y_center - bbox.height/2 * self._head_height),
+            ],
+            codes=[
+                Path.MOVETO,
+                Path.CURVE3,
+                Path.CURVE3
+            ]
+        )
+        style = ArrowStyle.CurveFilledB(
+            head_width=self._head_width, head_length=self._head_length
+        )
+        arrow = FancyArrowPatch(
+            path=path, arrowstyle=style, linewidth=self._line_width,
+            color="black"
+        )
+        axes.add_patch(arrow)
+        
+        if "note" in feature.qual:
+            axes.text(
+                x_center, y_center + bbox.height/4, feature.qual["note"],
+                color="black", ha="center", va="center",
+                size=9
+            )
+
+
+class TerminatorPlotter(FeaturePlotter):
+    """
+    A plotter for *regulatory* features with the *terminator* class.
+
+    Draws a vertical bar.
+
+    Parameters
+    ----------
+    bar_width : float, optional
+        The width of the line representing the bar.
+    """
+
+    def __init__(self, bar_width=5):
+        self._bar_width = bar_width
+
+    def matches(self, feature):
+        if feature.key == "regulatory":
+            if "regulatory_class" in feature.qual:
+                if feature.qual["regulatory_class"] == "terminator":
+                    return True
+        return False
+        
+    def draw(self, axes, feature, bbox, loc, style_param):
+
+        x = bbox.x0 + bbox.width/2
+
+        axes.plot(
+            (x, x), (bbox.y0, bbox.y1), color="black",
+            linestyle="-", linewidth=self._bar_width, marker="None"
+        )
+
+
+class RBSPlotter(FeaturePlotter):
+    """
+    A plotter for *regulatory* features with the
+    *ribosome_binding_site* class.
+
+    Draws an ellipse.
+
+    Parameters
+    ----------
+    height : float, optional
+        The width of the ellipse
+        as fraction of the feature drawing area height.
+    """
+
+    def __init__(self, height=0.4):
+        self._height = height
+
+    def matches(self, feature):
+        if feature.key == "regulatory":
+            if "regulatory_class" in feature.qual:
+                if feature.qual["regulatory_class"] == "ribosome_binding_site":
+                    return True
+        return False
+        
+    def draw(self, axes, feature, bbox, loc, style_param):
+        from matplotlib.patches import Ellipse
+
+        ellipse = Ellipse(
+            (bbox.x0 + bbox.width/2, bbox.y0 + bbox.height/2),
+            bbox.width, self._height*bbox.height,
+            color=colors["dimorange"], linewidth=0)
+        axes.add_patch(ellipse)

biotite/sequence/graphics/logo.py

@@ -0,0 +1,110 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.sequence.graphics"
+__author__ = "Patrick Kunzmann"
+__all__ = ["plot_sequence_logo"]
+
+import numpy as np
+from ...visualize import set_font_size_in_coord
+from ..alphabet import LetterAlphabet
+from .colorschemes import get_color_scheme
+import warnings
+from ..align import Alignment
+from .. import SequenceProfile
+
+
+def plot_sequence_logo(axes, profile, scheme=None, **kwargs):
+    """
+    Create a sequence logo. :footcite:`Schneider1990`
+
+    A sequence logo is visualizes the positional composition and
+    conservation of a profile encoded in the size of the letters.
+    Each position displays all symbols that are occurring at this
+    position stacked on each other, with their relative heights depicting
+    their relative frequency.
+    The height of such a stack depicts its conservation.
+    It is the maximum possible Shannon entropy of the alphabet
+    subtracted by the positional entropy.
+
+    Parameters
+    ----------
+    axes : Axes
+        The axes to draw the logo one.
+    profile: SequenceProfile
+        The logo is created based on this profile.
+    scheme : str or list of (tuple or str)
+        Either a valid color scheme name
+        (e.g. ``"rainbow"``, ``"clustalx"``, ``blossom``, etc.)
+        or a list of *Matplotlib* compatible colors.
+        The list length must be at least as long as the
+        length of the alphabet used by the `profile`.
+    **kwargs
+        Additional `text parameters <https://matplotlib.org/api/text_api.html#matplotlib.text.Text>`_.
+    
+    References
+    ----------
+    
+    .. footbibliography::
+    """
+    from matplotlib.text import Text
+
+    if isinstance(profile, Alignment):
+        warnings.warn("Using an alignment for this method is deprecated; use a profile instead", DeprecationWarning)
+        profile = SequenceProfile.from_alignment(profile)
+
+    alphabet = profile.alphabet
+    if not isinstance(alphabet, LetterAlphabet):
+        raise TypeError("The sequences' alphabet must be a letter alphabet")
+
+    if scheme is None:
+        colors = get_color_scheme("rainbow", alphabet)
+    elif isinstance(scheme, str):
+        colors = get_color_scheme(scheme, alphabet)
+    else:
+        colors = scheme
+    
+    # 'color' and 'size' property is not passed on to text
+    kwargs.pop("color", None)
+    kwargs.pop("size",  None)
+    
+    frequencies, entropies, max_entropy = _get_entropy(profile)
+    stack_heights = (max_entropy - entropies)
+    symbols_heights = stack_heights[:, np.newaxis] * frequencies
+    index_order = np.argsort(symbols_heights, axis=1)
+    for i in range(symbols_heights.shape[0]):
+        # Iterate over the alignment columns
+        index_order = np.argsort(symbols_heights)
+        start_height = 0
+        for j in index_order[i]:
+            # Stack the symbols at position on top of the preceeding one
+            height = symbols_heights[i,j]
+            if height > 0:
+                symbol = alphabet.decode(j)
+                text = axes.text(
+                    i+0.5, start_height, symbol,
+                    ha="left", va="bottom", color=colors[j],
+                    # Best results are obtained with this font size
+                    size=1,
+                    **kwargs
+                )
+                text.set_clip_on(True)
+                set_font_size_in_coord(text, width=1, height=height)
+                start_height += height
+
+    axes.set_xlim(0.5, len(profile.symbols)+0.5)
+    axes.set_ylim(0, max_entropy)
+
+
+def _get_entropy(profile):
+    freq = profile.symbols
+    freq = freq / np.sum(freq, axis=1)[:, np.newaxis]
+    # 0 * log2(0) = 0 -> Convert NaN to 0
+    no_zeros = freq != 0
+    pre_entropies = np.zeros(freq.shape)
+    pre_entropies[no_zeros] \
+        = freq[no_zeros] * np.log2(freq[no_zeros])
+    entropies = -np.sum(pre_entropies, axis=1)
+    max_entropy = np.log2(len(profile.alphabet))
+    return freq, entropies, max_entropy