<reponame>biocore/gneiss
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, gneiss development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import abc
from collections import namedtuple
from skbio import TreeNode
import pandas as pd
import numpy


class Dendrogram(TreeNode):
    """ Stores data to be plotted as a dendrogram.

    A `Dendrogram` object is represents a tree in addition to the
    key information required to create a tree layout prior to
    visualization.  No layouts are specified within this class,
    since this serves as a super class for different tree layouts.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth

    Notes
    -----
    `length` refers to the branch length of a node to its parent.
    `leafcount` is the number of tips within a subtree. `height` refers
    to the longest path from root to the deepst leaf in that subtree.
    `depth` is the number of nodes found in the longest path.

    """
    def __init__(self, use_lengths=True, **kwargs):
        """ Constructs a Dendrogram object for visualization.
        """
        super().__init__(**kwargs)

    def _cache_ntips(self):
        """ Counts the number of leaves under each subtree."""
        for n in self.postorder():
            if n.is_tip():
                n.leafcount = 1
            else:
                n.leafcount = sum(c.leafcount for c in n.children)

    def update_geometry(self, use_lengths, depth=None):
        """Calculate tree node attributes such as height and depth.

        Parameters
        ----------
        use_lengths: bool
           Specify if the branch length should be incorporated into
           the geometry calculations for visualization.
        depth: int
           The number of nodes in the longest path from root to leaf.

        This is agnostic to scale and orientation.
        """
        if self.length is None or not use_lengths:
            if depth is None:
                self.length = 0
            else:
                self.length = 1

        self.depth = (depth or 0) + self.length

        children = self.children
        if children:
            for c in children:
                c.update_geometry(use_lengths, self.depth)
            self.height = max([c.height for c in children]) + self.length
            self.leafcount = sum([c.leafcount for c in children])

        else:
            self.height = self.length
            self.leafcount = self.edgecount = 1

    def coords(self, height, width):
        """ Returns coordinates of nodes to be rendered in plot.

        Parameters
        ----------
        height : int
            The height of the canvas.
        width : int
            The width of the canvas.
        Returns
        -------
        pd.DataFrame
            index : str
                Name of node.
            x : float
                x-coordinate of node.
            y : float
                y-coordinate of node.
            child(i) : str
                Name of ith child node in that specific node.
                in the tree.
            is_tip : str
                Specifies if the node is a tip in the treee.
        """
        self.rescale(width, height)
        result = {}
        for node in self.postorder():
            children = {'child%d' % i: n.name
                        for i, n in enumerate(node.children)}
            coords = {'x': node.x2, 'y': node.y2}
            is_tip = {'is_tip': node.is_tip()}
            result[node.name] = {**coords, **children, **is_tip}
        result = pd.DataFrame(result).T

        # reorder so that x and y are first
        cols = ['x', 'y'] + sorted(list(set(result.columns) - set(['x', 'y'])))
        return result.loc[:, cols]

    @abc.abstractmethod
    def rescale(self, width, height):
        pass


class UnrootedDendrogram(Dendrogram):
    """ Stores data to be plotted as an unrooted dendrogram.

    A `UnrootedDendrogram` object is represents a tree in addition to the
    key information required to create a radial tree layout prior to
    visualization.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth
    """
    def __init__(self, **kwargs):
        """ Constructs a UnrootedDendrogram object for visualization.

        Parameters
        ----------
        use_lengths: bool
            Specifies if the branch lengths should be included in the
            resulting visualization (default True).
        """
        super().__init__(**kwargs)

    @classmethod
    def from_tree(cls, tree, use_lengths=True):
        """ Creates an UnrootedDendrogram object from a skbio tree.

        Parameters
        ----------
        tree : skbio.TreeNode
            Input skbio tree

        Returns
        -------
        UnrootedDendrogram
        """
        for n in tree.postorder():
            n.__class__ = UnrootedDendrogram

        tree.update_geometry(use_lengths)
        return tree

    def rescale(self, width, height):
        """ Find best scaling factor for fitting the tree in the figure.

        This method will find the best orientation and scaling possible
        to fit the tree within the dimensions specified by width and height.

        Parameters
        ----------
        width : float
            width of the canvas
        height : float
            height of the canvas

        Returns
        -------
        best_scaling : float
            largest scaling factor in which the tree can fit in the canvas.

        Notes
        -----
        """
        angle = (2 * numpy.pi) / self.leafcount
        # this loop is a horrible brute force hack
        # there are better (but complex) ways to find
        # the best rotation of the tree to fit the display.
        best_scale = 0
        for i in range(60):
            direction = i / 60.0 * numpy.pi
            # TODO:
            # This function has a little bit of recursion.  This will
            # need to be refactored to remove the recursion.

            points = self.update_coordinates(1.0, 0, 0, direction, angle)
            xs, ys = zip(*points)
            # double check that the tree fits within the margins
            scale = min(float(width) / (max(xs) - min(xs)),
                        float(height) / (max(ys) - min(ys)))
            # TODO: This margin seems a bit arbituary.
            # will need to investigate.
            scale *= 0.95  # extra margin for labels
            if scale > best_scale:
                best_scale = scale
                mid_x = width / 2 - ((max(xs) + min(xs)) / 2) * scale
                mid_y = height / 2 - ((max(ys) + min(ys)) / 2) * scale
                best_args = (scale, mid_x, mid_y, direction, angle)

        self.update_coordinates(*best_args)
        return best_scale

    def update_coordinates(self, s, x1, y1, a, da):
        """ Update x, y coordinates of tree nodes in canvas.

        `update_coordinates` will recursively updating the
        plotting parameters for all of the nodes within the tree.
        This can be applied when the tree becomes modified (i.e. pruning
        or collapsing) and the resulting coordinates need to be modified
        to reflect the changes to the tree structure.

        Parameters
        ----------
        s : float
            scaling
        x1 : float
            x midpoint
        y1 : float
            y midpoint
        a : float
            angle (degrees)
        da : float
            angle resolution (degrees)

        Returns
        -------
        points : list of tuple
            2D coordinates of all of the nodes.

        Notes
        -----
        This function has a little bit of recursion.  This will
        need to be refactored to remove the recursion.
        """
        # Constant angle algorithm.  Should add maximum daylight step.
        x2 = x1 + self.length * s * numpy.sin(a)
        y2 = y1 + self.length * s * numpy.cos(a)
        (self.x1, self.y1, self.x2, self.y2, self.angle) = (x1, y1, x2, y2, a)
        # TODO: Add functionality that allows for collapsing of nodes
        a = a - self.leafcount * da / 2
        if self.is_tip():
            points = [(x2, y2)]
        else:
            points = []
            # TODO:
            # This function has a little bit of recursion.  This will
            # need to be refactored to remove the recursion.
            for child in self.children:
                # calculate the arc that covers the subtree.
                ca = child.leafcount * da
                points += child.update_coordinates(s, x2, y2, a + ca / 2, da)
                a += ca
        return points


Dimensions = namedtuple('Dimensions', ['x', 'y', 'height'])


class RootedDendrogram(Dendrogram):
    """ Stores data to be plotted as an rooted dendrogram.

    A `RootedDendrogram` object is represents a tree in addition to the
    key information required to create a radial tree layout prior to
    visualization.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth
    """

    def width_required(self):
        return self.leafcount

    @abc.abstractmethod
    def xcoords(self, scale, x1):
        pass

    @abc.abstractmethod
    def ycoords(self, scale, y1):
        pass

    def rescale(self, width, height):
        """ Update x, y coordinates of tree nodes in canvas.

        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        xscale = width / self.height
        yscale = height / self.width_required()
        scale = Dimensions(xscale, yscale, self.height)

        # y coords done postorder, x preorder, y first.
        # so it has to be done in 2 passes.
        self.update_y_coordinates(scale)
        self.update_x_coordinates(scale)
        return xscale

    def update_y_coordinates(self, scale, y1=None):
        """The second pass through the tree.  Y coordinates only
        depend on the shape of the tree and yscale.

        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        if y1 is None:
            y1 = self.width_required() * scale.y
        child_y = y1
        for child in self.children:
            child.update_y_coordinates(scale, child_y)
            child_y -= child.width_required() * scale.y
        (self.y1, self.y2) = self.ycoords(scale, y1)

    def update_x_coordinates(self, scale, x1=0):
        """For non 'square' styles the x coordinates will depend
        (a bit) on the y coodinates, so they should be done first.
        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        (self.x1, self.x2) = self.xcoords(scale, x1)
        for child in self.children:
            child.update_x_coordinates(scale, self.x2)


class SquareDendrogram(RootedDendrogram):

    def ycoords(self, scale, y1):
        cys = [c.y1 for c in self.children]
        if cys:
            y2 = (cys[0] + cys[-1]) / 2.0
        else:
            y2 = y1 - 0.5 * scale.y
        return (y2, y2)

    def xcoords(self, scale, x1):
        if self.is_tip():
            return (x1, (scale.height - (self.height - self.length)) * scale.x)
        else:
            # give some margins for internal nodes
            dx = scale.x * self.length * 0.95
            x2 = x1 + dx
            return (x1, x2)

    @classmethod
    def from_tree(cls, tree):
        """ Creates an SquareDendrogram object from a skbio tree.

        Parameters
        ----------
        tree : skbio.TreeNode
            Input skbio tree
        Returns
        -------
        SquareDendrogram
        """
        for n in tree.postorder(include_self=True):
            n.__class__ = SquareDendrogram
        tree.update_geometry(use_lengths=False)
        return tree

# ----------------------------------------------------------------------------
# Copyright (c) 2016--, gneiss development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import abc
from collections import namedtuple
from skbio import TreeNode
import pandas as pd
import numpy


class Dendrogram(TreeNode):
    """ Stores data to be plotted as a dendrogram.

    A `Dendrogram` object is represents a tree in addition to the
    key information required to create a tree layout prior to
    visualization.  No layouts are specified within this class,
    since this serves as a super class for different tree layouts.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth

    Notes
    -----
    `length` refers to the branch length of a node to its parent.
    `leafcount` is the number of tips within a subtree. `height` refers
    to the longest path from root to the deepst leaf in that subtree.
    `depth` is the number of nodes found in the longest path.

    """
    def __init__(self, use_lengths=True, **kwargs):
        """ Constructs a Dendrogram object for visualization.
        """
        super().__init__(**kwargs)

    def _cache_ntips(self):
        """ Counts the number of leaves under each subtree."""
        for n in self.postorder():
            if n.is_tip():
                n.leafcount = 1
            else:
                n.leafcount = sum(c.leafcount for c in n.children)

    def update_geometry(self, use_lengths, depth=None):
        """Calculate tree node attributes such as height and depth.

        Parameters
        ----------
        use_lengths: bool
           Specify if the branch length should be incorporated into
           the geometry calculations for visualization.
        depth: int
           The number of nodes in the longest path from root to leaf.

        This is agnostic to scale and orientation.
        """
        if self.length is None or not use_lengths:
            if depth is None:
                self.length = 0
            else:
                self.length = 1

        self.depth = (depth or 0) + self.length

        children = self.children
        if children:
            for c in children:
                c.update_geometry(use_lengths, self.depth)
            self.height = max([c.height for c in children]) + self.length
            self.leafcount = sum([c.leafcount for c in children])

        else:
            self.height = self.length
            self.leafcount = self.edgecount = 1

    def coords(self, height, width):
        """ Returns coordinates of nodes to be rendered in plot.

        Parameters
        ----------
        height : int
            The height of the canvas.
        width : int
            The width of the canvas.
        Returns
        -------
        pd.DataFrame
            index : str
                Name of node.
            x : float
                x-coordinate of node.
            y : float
                y-coordinate of node.
            child(i) : str
                Name of ith child node in that specific node.
                in the tree.
            is_tip : str
                Specifies if the node is a tip in the treee.
        """
        self.rescale(width, height)
        result = {}
        for node in self.postorder():
            children = {'child%d' % i: n.name
                        for i, n in enumerate(node.children)}
            coords = {'x': node.x2, 'y': node.y2}
            is_tip = {'is_tip': node.is_tip()}
            result[node.name] = {**coords, **children, **is_tip}
        result = pd.DataFrame(result).T

        # reorder so that x and y are first
        cols = ['x', 'y'] + sorted(list(set(result.columns) - set(['x', 'y'])))
        return result.loc[:, cols]

    @abc.abstractmethod
    def rescale(self, width, height):
        pass


class UnrootedDendrogram(Dendrogram):
    """ Stores data to be plotted as an unrooted dendrogram.

    A `UnrootedDendrogram` object is represents a tree in addition to the
    key information required to create a radial tree layout prior to
    visualization.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth
    """
    def __init__(self, **kwargs):
        """ Constructs a UnrootedDendrogram object for visualization.

        Parameters
        ----------
        use_lengths: bool
            Specifies if the branch lengths should be included in the
            resulting visualization (default True).
        """
        super().__init__(**kwargs)

    @classmethod
    def from_tree(cls, tree, use_lengths=True):
        """ Creates an UnrootedDendrogram object from a skbio tree.

        Parameters
        ----------
        tree : skbio.TreeNode
            Input skbio tree

        Returns
        -------
        UnrootedDendrogram
        """
        for n in tree.postorder():
            n.__class__ = UnrootedDendrogram

        tree.update_geometry(use_lengths)
        return tree

    def rescale(self, width, height):
        """ Find best scaling factor for fitting the tree in the figure.

        This method will find the best orientation and scaling possible
        to fit the tree within the dimensions specified by width and height.

        Parameters
        ----------
        width : float
            width of the canvas
        height : float
            height of the canvas

        Returns
        -------
        best_scaling : float
            largest scaling factor in which the tree can fit in the canvas.

        Notes
        -----
        """
        angle = (2 * numpy.pi) / self.leafcount
        # this loop is a horrible brute force hack
        # there are better (but complex) ways to find
        # the best rotation of the tree to fit the display.
        best_scale = 0
        for i in range(60):
            direction = i / 60.0 * numpy.pi
            # TODO:
            # This function has a little bit of recursion.  This will
            # need to be refactored to remove the recursion.

            points = self.update_coordinates(1.0, 0, 0, direction, angle)
            xs, ys = zip(*points)
            # double check that the tree fits within the margins
            scale = min(float(width) / (max(xs) - min(xs)),
                        float(height) / (max(ys) - min(ys)))
            # TODO: This margin seems a bit arbituary.
            # will need to investigate.
            scale *= 0.95  # extra margin for labels
            if scale > best_scale:
                best_scale = scale
                mid_x = width / 2 - ((max(xs) + min(xs)) / 2) * scale
                mid_y = height / 2 - ((max(ys) + min(ys)) / 2) * scale
                best_args = (scale, mid_x, mid_y, direction, angle)

        self.update_coordinates(*best_args)
        return best_scale

    def update_coordinates(self, s, x1, y1, a, da):
        """ Update x, y coordinates of tree nodes in canvas.

        `update_coordinates` will recursively updating the
        plotting parameters for all of the nodes within the tree.
        This can be applied when the tree becomes modified (i.e. pruning
        or collapsing) and the resulting coordinates need to be modified
        to reflect the changes to the tree structure.

        Parameters
        ----------
        s : float
            scaling
        x1 : float
            x midpoint
        y1 : float
            y midpoint
        a : float
            angle (degrees)
        da : float
            angle resolution (degrees)

        Returns
        -------
        points : list of tuple
            2D coordinates of all of the nodes.

        Notes
        -----
        This function has a little bit of recursion.  This will
        need to be refactored to remove the recursion.
        """
        # Constant angle algorithm.  Should add maximum daylight step.
        x2 = x1 + self.length * s * numpy.sin(a)
        y2 = y1 + self.length * s * numpy.cos(a)
        (self.x1, self.y1, self.x2, self.y2, self.angle) = (x1, y1, x2, y2, a)
        # TODO: Add functionality that allows for collapsing of nodes
        a = a - self.leafcount * da / 2
        if self.is_tip():
            points = [(x2, y2)]
        else:
            points = []
            # TODO:
            # This function has a little bit of recursion.  This will
            # need to be refactored to remove the recursion.
            for child in self.children:
                # calculate the arc that covers the subtree.
                ca = child.leafcount * da
                points += child.update_coordinates(s, x2, y2, a + ca / 2, da)
                a += ca
        return points


Dimensions = namedtuple('Dimensions', ['x', 'y', 'height'])


class RootedDendrogram(Dendrogram):
    """ Stores data to be plotted as an rooted dendrogram.

    A `RootedDendrogram` object is represents a tree in addition to the
    key information required to create a radial tree layout prior to
    visualization.

    Parameters
    ----------
    use_lengths: bool
        Specifies if the branch lengths should be included in the
        resulting visualization (default True).

    Attributes
    ----------
    length
    leafcount
    height
    depth
    """

    def width_required(self):
        return self.leafcount

    @abc.abstractmethod
    def xcoords(self, scale, x1):
        pass

    @abc.abstractmethod
    def ycoords(self, scale, y1):
        pass

    def rescale(self, width, height):
        """ Update x, y coordinates of tree nodes in canvas.

        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        xscale = width / self.height
        yscale = height / self.width_required()
        scale = Dimensions(xscale, yscale, self.height)

        # y coords done postorder, x preorder, y first.
        # so it has to be done in 2 passes.
        self.update_y_coordinates(scale)
        self.update_x_coordinates(scale)
        return xscale

    def update_y_coordinates(self, scale, y1=None):
        """The second pass through the tree.  Y coordinates only
        depend on the shape of the tree and yscale.

        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        if y1 is None:
            y1 = self.width_required() * scale.y
        child_y = y1
        for child in self.children:
            child.update_y_coordinates(scale, child_y)
            child_y -= child.width_required() * scale.y
        (self.y1, self.y2) = self.ycoords(scale, y1)

    def update_x_coordinates(self, scale, x1=0):
        """For non 'square' styles the x coordinates will depend
        (a bit) on the y coodinates, so they should be done first.
        Parameters
        ----------
        scale : Dimensions
            Scaled dimensions of the tree
        x1 : int
            X-coordinate of parent
        """
        (self.x1, self.x2) = self.xcoords(scale, x1)
        for child in self.children:
            child.update_x_coordinates(scale, self.x2)


class SquareDendrogram(RootedDendrogram):

    def ycoords(self, scale, y1):
        cys = [c.y1 for c in self.children]
        if cys:
            y2 = (cys[0] + cys[-1]) / 2.0
        else:
            y2 = y1 - 0.5 * scale.y
        return (y2, y2)

    def xcoords(self, scale, x1):
        if self.is_tip():
            return (x1, (scale.height - (self.height - self.length)) * scale.x)
        else:
            # give some margins for internal nodes
            dx = scale.x * self.length * 0.95
            x2 = x1 + dx
            return (x1, x2)

    @classmethod
    def from_tree(cls, tree):
        """ Creates an SquareDendrogram object from a skbio tree.

        Parameters
        ----------
        tree : skbio.TreeNode
            Input skbio tree
        Returns
        -------
        SquareDendrogram
        """
        for n in tree.postorder(include_self=True):
            n.__class__ = SquareDendrogram
        tree.update_geometry(use_lengths=False)
        return tree
# ---------------------------------------------------------------------------- # Copyright (c) 2016--, gneiss development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file COPYING.txt, distributed with this software. # ---------------------------------------------------------------------------- Stores data to be plotted as a dendrogram.      A `Dendrogram` object is represents a tree in addition to the     key information required to create a tree layout prior to     visualization.  No layouts are specified within this class,     since this serves as a super class for different tree layouts.      Parameters     ----------     use_lengths: bool         Specifies if the branch lengths should be included in the         resulting visualization (default True).      Attributes     ----------     length     leafcount     height     depth      Notes     -----     `length` refers to the branch length of a node to its parent.     `leafcount` is the number of tips within a subtree. `height` refers     to the longest path from root to the deepst leaf in that subtree.     `depth` is the number of nodes found in the longest path. Constructs a Dendrogram object for visualization. Counts the number of leaves under each subtree. Calculate tree node attributes such as height and depth.          Parameters         ----------         use_lengths: bool            Specify if the branch length should be incorporated into            the geometry calculations for visualization.         depth: int            The number of nodes in the longest path from root to leaf.          This is agnostic to scale and orientation. Returns coordinates of nodes to be rendered in plot.          Parameters         ----------         height : int             The height of the canvas.         width : int             The width of the canvas.         Returns         -------         pd.DataFrame             index : str                 Name of node.             x : float                 x-coordinate of node.             y : float                 y-coordinate of node.             child(i) : str                 Name of ith child node in that specific node.                 in the tree.             is_tip : str                 Specifies if the node is a tip in the treee. # reorder so that x and y are first Stores data to be plotted as an unrooted dendrogram.      A `UnrootedDendrogram` object is represents a tree in addition to the     key information required to create a radial tree layout prior to     visualization.      Parameters     ----------     use_lengths: bool         Specifies if the branch lengths should be included in the         resulting visualization (default True).      Attributes     ----------     length     leafcount     height     depth Constructs a UnrootedDendrogram object for visualization.          Parameters         ----------         use_lengths: bool             Specifies if the branch lengths should be included in the             resulting visualization (default True). Creates an UnrootedDendrogram object from a skbio tree.          Parameters         ----------         tree : skbio.TreeNode             Input skbio tree          Returns         -------         UnrootedDendrogram Find best scaling factor for fitting the tree in the figure.          This method will find the best orientation and scaling possible         to fit the tree within the dimensions specified by width and height.          Parameters         ----------         width : float             width of the canvas         height : float             height of the canvas          Returns         -------         best_scaling : float             largest scaling factor in which the tree can fit in the canvas.          Notes         ----- # this loop is a horrible brute force hack # there are better (but complex) ways to find # the best rotation of the tree to fit the display. # TODO: # This function has a little bit of recursion.  This will # need to be refactored to remove the recursion. # double check that the tree fits within the margins # TODO: This margin seems a bit arbituary. # will need to investigate. # extra margin for labels Update x, y coordinates of tree nodes in canvas.          `update_coordinates` will recursively updating the         plotting parameters for all of the nodes within the tree.         This can be applied when the tree becomes modified (i.e. pruning         or collapsing) and the resulting coordinates need to be modified         to reflect the changes to the tree structure.          Parameters         ----------         s : float             scaling         x1 : float             x midpoint         y1 : float             y midpoint         a : float             angle (degrees)         da : float             angle resolution (degrees)          Returns         -------         points : list of tuple             2D coordinates of all of the nodes.          Notes         -----         This function has a little bit of recursion.  This will         need to be refactored to remove the recursion. # Constant angle algorithm.  Should add maximum daylight step. # TODO: Add functionality that allows for collapsing of nodes # TODO: # This function has a little bit of recursion.  This will # need to be refactored to remove the recursion. # calculate the arc that covers the subtree. Stores data to be plotted as an rooted dendrogram.      A `RootedDendrogram` object is represents a tree in addition to the     key information required to create a radial tree layout prior to     visualization.      Parameters     ----------     use_lengths: bool         Specifies if the branch lengths should be included in the         resulting visualization (default True).      Attributes     ----------     length     leafcount     height     depth Update x, y coordinates of tree nodes in canvas.          Parameters         ----------         scale : Dimensions             Scaled dimensions of the tree         x1 : int             X-coordinate of parent # y coords done postorder, x preorder, y first. # so it has to be done in 2 passes. The second pass through the tree.  Y coordinates only         depend on the shape of the tree and yscale.          Parameters         ----------         scale : Dimensions             Scaled dimensions of the tree         x1 : int             X-coordinate of parent For non 'square' styles the x coordinates will depend         (a bit) on the y coodinates, so they should be done first.         Parameters         ----------         scale : Dimensions             Scaled dimensions of the tree         x1 : int             X-coordinate of parent # give some margins for internal nodes Creates an SquareDendrogram object from a skbio tree.          Parameters         ----------         tree : skbio.TreeNode             Input skbio tree         Returns         -------         SquareDendrogram