cocoatree 0.1.0__py3-none-any.whl

cocoatree/visualization.py

@@ -0,0 +1,440 @@
+"""Module to visualize phylogenetic trees along with XCoRs"""
+
+# User provided file:
+# - phylogenetic tree in newick format
+# - multiple sequence alignment used to generate the tree in fasta format
+# - annotation table in csv format
+
+# Import necessary packages
+from ete3 import ProfileFace, TreeStyle, NodeStyle, TextFace, \
+    add_face_to_node, SeqMotifFace, RectFace
+from pandas.api.types import is_numeric_dtype  # type: ignore
+import pandas as pd
+import numpy as np
+from PyQt5 import QtGui
+import matplotlib.colors as colors
+import matplotlib.cm as cmx
+import matplotlib.pyplot as plt
+
+from .msa import compute_seq_identity, compute_seq_similarity, \
+    compute_normalized_seq_similarity
+
+
+def _annot_to_color(attribute, tree, df_annot, cmap='jet'):
+    """
+    Reads in the attributes specified by the user in the annotation csv file
+    and attributes a color palette for each.
+
+    Parameters
+    ----------
+    tree : ete3's tree object,
+            as imported by io.load_tree_ete3()
+
+    attributes : list of column names to grab
+
+    df_annot : pandas dataframe of the annotation file
+
+    Returns
+    -------
+    att_dict : dictionnary in which keys are the sequence IDs and the values
+            are the colors associated with it
+
+    color_dict : dictionnary in which keys are the attribute's categories and
+            the values are the colors associated to each category
+    """
+    id_lst = tree.get_leaf_names()
+    df_annot = df_annot.fillna('unknown')
+    if is_numeric_dtype(df_annot['Seq_ID']):
+        df_annot['Seq_ID'] = df_annot['Seq_ID'].astype('str')
+    df_annot = df_annot[df_annot['Seq_ID'].isin(id_lst)]
+
+    att_dict = {}
+    df_annot = df_annot[['Seq_ID', attribute]]
+
+    if isinstance(cmap, str):
+        color_dict = _get_color_palette(
+            list(df_annot[attribute].unique()), cmap)
+    else:
+        color_dict = {n: cmap[n] for n in list(df_annot[attribute].unique())}
+
+    df_annot[str(attribute + '_color')] = df_annot.apply(
+        lambda row: color_dict[row[attribute]], axis=1)
+    for i in range(0, len(df_annot['Seq_ID'])):
+        row = df_annot.iloc[i].tolist()
+        att_dict[row[0]] = row[2]
+
+    return att_dict, color_dict
+
+
+def _generate_colors_from_colormaps(n_colors, cmap="jet", as_hex=True):
+    """
+    Generate a list of n colors from colormap
+    """
+
+    colormap = plt.get_cmap(str(cmap))
+    indx = np.linspace(0, 1, n_colors)
+    indexed_colors = [colormap(i) for i in indx]
+    if as_hex:
+        indexed_colors = [colors.to_hex(i) for i in indexed_colors]
+    return indexed_colors
+
+
+# TO DO: allow user to choose which color to use for 'unknown'
+# (currently: white by default)
+def _get_color_palette(values, cmap):
+
+    nvals = len(values)
+    colors = _generate_colors_from_colormaps(nvals, cmap=cmap, as_hex=True)
+
+    color_dict = {}  # key = value, value = colour id
+    for i in range(0, nvals):
+        if values[i] == 'unknown':
+            color_dict[values[i]] = '#FFFFFF'
+        else:
+            color_dict[values[i]] = colors[i]
+
+    return color_dict
+
+
+def _get_color_gradient(self):
+    """
+    Function which allows to use matplotlib colormaps in ete3 heatmap
+    Adapted from:
+    https://github.com/lthiberiol/virfac/blob/master/get_color_gradient.py
+    """
+    cNorm = colors.Normalize(vmin=0, vmax=1)
+    scalarMap = cmx.ScalarMappable(norm=cNorm,
+                                   cmap=plt.get_cmap(self.colorscheme))
+    color_scale = []
+    for scale in np.linspace(0, 1, 201):
+        [r, g, b, a] = scalarMap.to_rgba(scale, bytes=True)
+        color_scale.append(QtGui.QColor(r, g, b, a))
+
+    return color_scale
+
+
+def update_tree_ete3_and_return_style(
+        tree_ete3, df_annot,
+        xcor_id=None,
+        xcor_seq=None,
+        meta_data=None,
+        show_leaf_name=True,
+        fig_title='',
+        linewidth=1,
+        linecolor="#000000",
+        bootstrap_style={},
+        tree_scale=200,
+        metadata_colors=None,
+        t_xcor_seq=False,
+        t_xcor_heatmap=False,
+        matrix_type='identity',
+        colormap='inferno'
+        ):
+    """
+    Update ete3 tree with XCoR info and attributes and return tree_style for
+    further visualization.
+
+    Parameters
+    ----------
+    tree_ete3 : ete3's tree object,
+            as imported by io.load_tree_ete3()
+
+    annot_file : pandas dataframe of the annotation file
+
+    xcor_id : list of XCoR sequence identifiers, as imported by io.load_msa()
+            the ids must match with the tree's leaves id
+
+    xcor_seq : corresponding list of xcor sequences to display,
+            as imported by io.load_msa()
+
+    meta_data : tuple of annotations to display
+                 (from annotation file's header)
+
+    show_leaf_name : boolean, optional, default: True
+        whether to show leaf names.
+
+    linewidth : int, optional, default: 1
+        width of the lines in the tree
+
+    linecolor : str, optional, default: "#000000"
+        color of the lines
+
+    bootstrap_style : dict, optional,
+        `fgcolor`: color of the bootstrap node, default: "darkred"
+        `size`: size of the bootstrap node, default: 10
+        `support`: int between 0 and 100, minimum support level for display
+
+    tree_scale : int, optional, default: 200
+        sets the scale of the tree in ETE3: the higher, the larger the tree
+        will be (in width)
+
+    metadata_colors : dict, str, or None, optional, default: None
+        colors for the metadata:
+            - None: generates automatically the colors
+            - str: uses a Matplotlib colormap to generate the colors
+            - dict: specifies colors for each matadata entry
+                {key: color}
+
+    fig_title : figure title (str)
+
+    t_xcor_seq : boolean,
+        whether to show the sequences of the XCoR
+
+    t_xcor_heatmap : boolean,
+        whether to add a heatmap of the identity or similarity matrix between
+        XCoR sequences
+
+    matrix_type : str, default='identity'
+        whether to compute pairwise sequence identity ('identity'), similarity
+        ('similarity'), or normalized similarity ('norm_similarity').
+
+    colormap : str, default='inferno'
+        the matplotlib colormap to use for the heatmap
+
+    Returns
+    -------
+    tree_style : TreeStyle class from ete3
+
+    column_end : int, the number of columns after the tree. If you want to
+        plot anything else alongside the tree, the column number should be
+        equal to this value.
+
+    """
+
+    tree_style = TreeStyle()
+    tree_style.scale = tree_scale
+    tree_style.layout_fn = []
+    # tree_style.branch_vertical_margin = 20
+    tree_style.show_leaf_name = show_leaf_name
+
+    # Add bootstrap support NodeStyle
+    boot_style = NodeStyle()
+    boot_style["fgcolor"] = \
+        bootstrap_style["fgcolor"] if "fgcolor" in bootstrap_style \
+        else "darkred"
+    boot_style["size"] = \
+        bootstrap_style["size"] if "size" in bootstrap_style else 10
+    support = \
+        bootstrap_style["support"] if "support" in bootstrap_style else 95
+
+    boot_style["hz_line_width"] = linewidth
+    boot_style["vt_line_width"] = linewidth
+    boot_style["vt_line_color"] = linecolor
+    boot_style["hz_line_color"] = linecolor
+
+    empty_style = NodeStyle()
+    empty_style["size"] = 0
+    empty_style["vt_line_width"] = linewidth
+    empty_style["hz_line_width"] = linewidth
+    empty_style["vt_line_color"] = linecolor
+    empty_style["hz_line_color"] = linecolor
+
+    for node in tree_ete3.traverse():
+        if node.support >= support:
+            node.set_style(boot_style)
+        else:
+            node.set_style(empty_style)
+
+    column_layout = 0
+    col_legend_rectface = 0
+
+    if metadata_colors is None:
+        metadata_colors = "jet"
+
+    # If no metadata, do nothing
+    if meta_data:
+
+        def layout_attribute(node, column=column_layout):
+            if node.is_leaf():
+                name = node.name
+                rect_faces = [None for i in range(len(meta_data))]
+                for i, col in enumerate(meta_data):
+                    colors, _ = _annot_to_color(col,
+                                                tree_ete3,
+                                                df_annot,
+                                                cmap=metadata_colors)
+
+                    rect_faces[i] = RectFace(50, 20,
+                                             fgcolor=colors[name],
+                                             bgcolor=colors[name])
+                    rect_faces[i].margin_left = 5
+                    rect_faces[i].margin_right = 0
+                    if i == len(meta_data) - 1:
+                        rect_faces[i].margin_right = 30
+                    add_face_to_node(rect_faces[i], node, column=column,
+                                     position='aligned')
+                    column += 1
+
+        tree_style.layout_fn.append(layout_attribute)
+
+        # Add legend
+        legend_face = [None for i in range(len(meta_data))]
+        for i, col in enumerate(meta_data):
+            _, col_dict = _annot_to_color(col, tree_ete3,
+                                          df_annot, cmap=metadata_colors)
+            tree_style.legend.add_face(TextFace(col,
+                                                fsize=10,
+                                                bold=True),
+                                       column=col_legend_rectface)
+            # otherwise text is not in front of RectFace
+            tree_style.legend.add_face(TextFace(""),
+                                       column=col_legend_rectface + 1)
+
+            legend_face[i] = {key: None for key in col_dict.keys()}
+            for key in col_dict.keys():
+                legend_face[i][key] = RectFace(50, 20, fgcolor=col_dict[key],
+                                               bgcolor=col_dict[key])
+                legend_face[i][key].margin_right = 5
+                legend_face[i][key].margin_left = 10
+                tree_style.legend.add_face(legend_face[i][key],
+                                           column=col_legend_rectface)
+                tree_style.legend.add_face(TextFace(key, fsize=10),
+                                           column=col_legend_rectface + 1)
+            col_legend_rectface += 2
+    column_layout += len(meta_data) if meta_data else 0
+
+    if t_xcor_seq:
+        tree_style, column_layout = add_xcor_sequences_to_tree(
+            tree_style, tree_ete3, xcor_id,
+            xcor_seq, column_start=column_layout)
+
+    if t_xcor_heatmap:
+        tree_style, column_layout = add_heatmap_to_tree(
+            tree_style, tree_ete3, xcor_id, xcor_seq,
+            matrix_type=matrix_type,
+            column_start=column_layout, colormap=colormap)
+
+    # Add title
+    tree_style.title.add_face(TextFace(fig_title, fsize=20), column=0)
+
+    return tree_style, column_layout
+
+
+def add_xcor_sequences_to_tree(tree_style, tree_ete3, xcor_id, xcor_seq,
+                               column_start=0):
+    """
+    Add XCoR sequence to ETE3's tree style
+
+    Parameters
+    ----------
+    tree_style : ETE3's tree_style object
+
+    tree_ete3 : ete3's tree object,
+            as imported by io.load_tree_ete3()
+
+    xcor_id : list of XCoR sequence identifiers, as imported by io.load_msa()
+            the ids must match with the tree's leaves id
+
+    xcor_seq : corresponding list of XCoR sequences to display,
+            as imported by io.load_msa()
+
+    column_start : int, optional, default : 0
+        the column on which to start plotting
+
+    Returns
+    -------
+    tree_style : TreeStyle class from ete3
+
+    column_end : int, the number of columns after the tree. If you want to
+        plot anything else alongside the tree, the column number should be
+        equal to this value.
+
+    """
+    xcor_dict = {
+        xcor_id[i]: str(xcor_seq[i]) for i in range(len(xcor_id))}
+
+    def layout_SeqMotifFace(node, column=column_start):
+        if node.is_leaf():
+            if node.name in xcor_dict:
+                seq = xcor_dict[node.name]
+            else:
+                seq = '-' * len(xcor_seq[0])
+            seqFace = SeqMotifFace(seq,
+                                   motifs=[[0, len(xcor_seq[0]), "seq",
+                                            20, 20, None, None, None]],
+                                   scale_factor=1)
+            seqFace.margin_right = 30
+            add_face_to_node(seqFace, node, column=column,
+                             position='aligned')
+    tree_style.layout_fn.append(layout_SeqMotifFace)
+    column_start += 1
+    return tree_style, column_start
+
+
+def add_heatmap_to_tree(tree_style, tree_ete3, xcor_id, xcor_seq,
+                        matrix_type="identity",
+                        column_start=0, width=20, colormap="inferno"):
+    """
+    Add heatmap to ETE3's tree style
+
+    Parameters
+    ----------
+    tree_style : ETE3's tree_style object
+
+    tree_ete3 : ete3's tree object,
+            as imported by io.load_tree_ete3()
+
+    xcor_id : list of XCoR sequence identifiers, as imported by io.load_msa()
+            the ids must match with the tree's leaves id
+
+    xcor_seq : corresponding list of XCoR sequences to display,
+            as imported by io.load_msa()
+
+    matrix_type : str, default='identity'
+            whether to compute pairwise matrix identity ('identity'),
+            similarity ('similarity'), or normalized similarity
+            ('norm_similarity')
+
+    column_start : int, optional, default : 0
+        the column on which to start plotting
+
+    width : int, optional, default : 20
+        the width of each square of the heatmap. If width == 20, the heatmap
+        will be squared.
+
+    colormap : str, optional, default: "inferno"
+        any Matplotlib's colormap
+
+    Returns
+    -------
+    tree_style : TreeStyle class from ete3
+
+    column_end : int, the number of columns after the tree. If you want to
+        plot anything else alongside the tree, the column number should be
+        equal to this value.
+    """
+
+    leaves_id = tree_ete3.get_leaf_names()
+    nb_leaves = len(leaves_id)
+
+    # allow to chose among Matplotlib's colormaps
+    ProfileFace.get_color_gradient = _get_color_gradient
+
+    # Check that sequences in the similarity matrix are ordered as in the
+    # tree leaves and keep only sequences that are present in the tree
+    sequences = pd.DataFrame(index=xcor_id, data={"seq": xcor_seq})
+    reordered_sequences = sequences.loc[leaves_id, "seq"].values
+
+    if matrix_type == 'identity':
+        matrix = compute_seq_identity(reordered_sequences)
+    elif matrix_type == 'similarity':
+        matrix = compute_seq_similarity(reordered_sequences)
+    elif matrix_type == 'norm_similarity':
+        matrix = compute_normalized_seq_similarity(reordered_sequences)
+    # FIX to zero values appearing black in the heatmap whatever the cmap
+    matrix[matrix == 0] = 0.00000001
+    min_v = float(np.min(matrix))
+    max_v = float(np.max(matrix))
+    center_v = float(np.mean([min_v, max_v]))
+
+    # Add heatmap profile to each leaf
+    for i, lf in enumerate(tree_ete3.iter_leaves()):
+        lf.add_features(profile=matrix[i])
+        lf.add_features(deviation=[0 for x in range(matrix.shape[0])])
+        lf.add_face(ProfileFace(max_v=max_v, min_v=min_v, center_v=center_v,
+                                width=(nb_leaves*width), height=20,
+                                style='heatmap',
+                                colorscheme=colormap),
+                    column=column_start, position="aligned")
+    column_start += nb_leaves*width
+    return tree_style, column_start

cocoatree-0.1.0.dist-info/METADATA

@@ -0,0 +1,66 @@
+Metadata-Version: 2.4
+Name: cocoatree
+Version: 0.1.0
+Summary: Awesome coevolution stuff
+Author: 
+License: MIT
+Project-URL: Bug Reports, https://github.com/FIXME
+Project-URL: Source, https://github.com/FIXME/
+Keywords: coevolution,MSA
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: <4.0,>=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Provides-Extra: dev
+Requires-Dist: flake8; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Dynamic: license-file
+
+# COCOA-Tree: COllaborative COevolution Analysis Toolbox
+
+**COCOA-Tree** is a Python library to perform coevolution analyses of proteins and integrate phylogenetic information
+to better understand the coevolution signals.
+
+It regroups various coevolution metrics and corrections, such as statistical coevolution analysis (SCA) or mutual
+information (MI).
+
+Website: [tree-bioinfo-intra.timc.fr/projects/cocoa/](http://tree-bioinfo-intra.timc.fr/projects/cocoa/index.html)
+
+## Library organization
+
+COCOA-Tree is organized in several modules, each allowing to perform different tasks of a coevolution analysis
+pipeline:
+
+[cocoatree_orga](../cocoatree_orga.pdf)
+
+## Installation
+
+### Dependencies
+
+COCOA-Tree requires:
+- Python (>= 3.9)
+- NumPy
+- scikit-learn
+- biopython
+- ete3
+
+Matplotlib is also required for running the examples.
+
+### User installation
+
+To install for development purposes, use::
+
+    python setup.py develop
+
+
+All changes in the python module will be repercuted on the installed version
+(in practice the installed version is a symlink towards the package in
+development).
+

cocoatree-0.1.0.dist-info/RECORD

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+cocoatree-0.1.0.dist-info/licenses/LICENSE,sha256=-csX-kOWZ0Ew72OZUq6Dpl7zF7FbxzMuib6ItKxEpZw,1496
+cocoatree-0.1.0.dist-info/METADATA,sha256=MjEZVwFEqMXZXntqHGK-E1GSG4syibLxzk7_ImZ695Q,1874
+cocoatree-0.1.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+cocoatree-0.1.0.dist-info/top_level.txt,sha256=1gUOukKDkF8RMx0GztzKIDHtoWbqc6ChHpZGUOl-D2M,10
+cocoatree-0.1.0.dist-info/RECORD,,

cocoatree-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.10.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

cocoatree-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,28 @@
+Copyright (c) 2025 The COCOA-Tree developers.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.

cocoatree-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+cocoatree