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Plot the given tree using matplotlib (or pylab). The graphic is a rooted tree, drawn with roughly the same algorithm as draw_ascii. Additional keyword arguments passed into this function are used as pyplot options. The input format should be in the form of: pyplot_option_name=(tuple), pyplot_option_name=(tuple, dict), or pyplot_option_name=(dict). (more...)
def draw(tree, label_func=str, do_show=True, show_confidence=True, # For power users axes=None, branch_labels=None, *args, **kwargs): """Plot the given tree using matplotlib (or pylab). The graphic is a rooted tree, drawn with roughly the same algorithm as draw_ascii. Additional keyword arguments passed into this function are used as pyplot options. The input format should be in the form of: pyplot_option_name=(tuple), pyplot_option_name=(tuple, dict), or pyplot_option_name=(dict). Example using the pyplot options 'axhspan' and 'axvline': >>> Phylo.draw(tree, axhspan=((0.25, 7.75), {'facecolor':'0.5'}), ... axvline={'x':'0', 'ymin':'0', 'ymax':'1'}) Visual aspects of the plot can also be modified using pyplot's own functions and objects (via pylab or matplotlib). In particular, the pyplot.rcParams object can be used to scale the font size (rcParams["font.size"]) and line width (rcParams["lines.linewidth"]). :Parameters: label_func : callable A function to extract a label from a node. By default this is str(), but you can use a different function to select another string associated with each node. If this function returns None for a node, no label will be shown for that node. do_show : bool Whether to show() the plot automatically. show_confidence : bool Whether to display confidence values, if present on the tree. axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created. branch_labels : dict or callable A mapping of each clade to the label that will be shown along the branch leading to it. By default this is the confidence value(s) of the clade, taken from the ``confidence`` attribute, and can be easily toggled off with this function's ``show_confidence`` option. But if you would like to alter the formatting of confidence values, or label the branches with something other than confidence, then use this option. """ try: import matplotlib.pyplot as plt except ImportError: try: import pylab as plt except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install matplotlib or pylab if you want to use draw.") import matplotlib.collections as mpcollections # Arrays that store lines for the plot of clades horizontal_linecollections = [] vertical_linecollections = [] # Options for displaying branch labels / confidence def conf2str(conf): if int(conf) == conf: return str(int(conf)) return str(conf) if not branch_labels: if show_confidence: def format_branch_label(clade): if hasattr(clade, 'confidences'): # phyloXML supports multiple confidences return '/'.join(conf2str(cnf.value) for cnf in clade.confidences) if clade.confidence: return conf2str(clade.confidence) return None else: def format_branch_label(clade): return None elif isinstance(branch_labels, dict): def format_branch_label(clade): return branch_labels.get(clade) else: assert callable(branch_labels), \ "branch_labels must be either a dict or a callable (function)" format_branch_label = branch_labels # Layout def get_x_positions(tree): """Create a mapping of each clade to its horizontal position. Dict of {clade: x-coord} """ depths = tree.depths() # If there are no branch lengths, assume unit branch lengths if not max(depths.values()): depths = tree.depths(unit_branch_lengths=True) return depths def get_y_positions(tree): """Create a mapping of each clade to its vertical position. Dict of {clade: y-coord}. Coordinates are negative, and integers for tips. """ maxheight = tree.count_terminals() # Rows are defined by the tips heights = dict((tip, maxheight - i) for i, tip in enumerate(reversed(tree.get_terminals()))) # Internal nodes: place at midpoint of children def calc_row(clade): for subclade in clade: if subclade not in heights: calc_row(subclade) # Closure over heights heights[clade] = (heights[clade.clades[0]] + heights[clade.clades[-1]]) / 2.0 if tree.root.clades: calc_row(tree.root) return heights x_posns = get_x_positions(tree) y_posns = get_y_positions(tree) # The function draw_clade closes over the axes object if axes is None: fig = plt.figure() axes = fig.add_subplot(1, 1, 1) elif not isinstance(axes, plt.matplotlib.axes.Axes): raise ValueError("Invalid argument for axes: %s" % axes) def draw_clade_lines(use_linecollection=False, orientation='horizontal', y_here=0, x_start=0, x_here=0, y_bot=0, y_top=0, color='black', lw='.1'): """Create a line with or without a line collection object. Graphical formatting of the lines representing clades in the plot can be customized by altering this function. """ if (use_linecollection==False and orientation=='horizontal'): axes.hlines(y_here, x_start, x_here, color=color, lw=lw) elif (use_linecollection==True and orientation=='horizontal'): horizontal_linecollections.append(mpcollections.LineCollection( [[(x_start, y_here), (x_here, y_here)]], color=color, lw=lw),) elif (use_linecollection==False and orientation=='vertical'): axes.vlines(x_here, y_bot, y_top, color=color) elif (use_linecollection==True and orientation=='vertical'): vertical_linecollections.append(mpcollections.LineCollection( [[(x_here, y_bot), (x_here, y_top)]], color=color, lw=lw),) def draw_clade(clade, x_start, color, lw): """Recursively draw a tree, down from the given clade.""" x_here = x_posns[clade] y_here = y_posns[clade] # phyloXML-only graphics annotations if hasattr(clade, 'color') and clade.color is not None: color = clade.color.to_hex() if hasattr(clade, 'width') and clade.width is not None: lw = clade.width * plt.rcParams['lines.linewidth'] # Draw a horizontal line from start to here draw_clade_lines(use_linecollection=True, orientation='horizontal', y_here=y_here, x_start=x_start, x_here=x_here, color=color, lw=lw) # Add node/taxon labels label = label_func(clade) if label not in (None, clade.__class__.__name__): axes.text(x_here, y_here, ' %s' % label, verticalalignment='center') # Add label above the branch (optional) conf_label = format_branch_label(clade) if conf_label: axes.text(0.5*(x_start + x_here), y_here, conf_label, fontsize='small', horizontalalignment='center') if clade.clades: # Draw a vertical line connecting all children y_top = y_posns[clade.clades[0]] y_bot = y_posns[clade.clades[-1]] # Only apply widths to horizontal lines, like Archaeopteryx draw_clade_lines(use_linecollection=True, orientation='vertical', x_here=x_here, y_bot=y_bot, y_top=y_top, color=color, lw=lw) # Draw descendents for child in clade: draw_clade(child, x_here, color, lw) draw_clade(tree.root, 0, 'k', plt.rcParams['lines.linewidth']) # If line collections were used to create clade lines, here they are added # to the pyplot plot. for i in horizontal_linecollections: axes.add_collection(i) for i in vertical_linecollections: axes.add_collection(i) # Aesthetics if hasattr(tree, 'name') and tree.name: axes.set_title(tree.name) axes.set_xlabel('branch length') axes.set_ylabel('taxa') # Add margins around the tree to prevent overlapping the axes xmax = max(x_posns.values()) axes.set_xlim(-0.05 * xmax, 1.25 * xmax) # Also invert the y-axis (origin at the top) # Add a small vertical margin, but avoid including 0 and N+1 on the y axis axes.set_ylim(max(y_posns.values()) + 0.8, 0.2) # Parse and process key word arguments as pyplot options for key, value in kwargs.items(): try: # Check that the pyplot option input is iterable, as required [i for i in value] except TypeError: raise ValueError('Keyword argument "%s=%s" is not in the format ' 'pyplot_option_name=(tuple), pyplot_option_name=(tuple, dict),' ' or pyplot_option_name=(dict) ' % (key, value)) if isinstance(value, dict): getattr(plt, str(key))(**dict(value)) elif not (isinstance(value[0], tuple)): getattr(plt, str(key))(*value) elif (isinstance(value[0], tuple)): getattr(plt, str(key))(*value[0], **dict(value[1])) if do_show: plt.show()
tree.ladderize() pylab.rcParams["lines.linewidth"] = 3.0 Phylo.draw(tree, do_show=False) pylab.savefig(out_file)
src/b/i/biopython-HEAD/Tests/test_Phylo_depend.py biopython(Download)
dollo = Phylo.read(EX_DOLLO, 'phyloxml') apaf = Phylo.read(EX_APAF, 'phyloxml') Phylo.draw(dollo, do_show=False) Phylo.draw(apaf, do_show=False) # Fancier options Phylo.draw(apaf, do_show=False, branch_labels={apaf.root: 'Root'}) Phylo.draw(apaf, do_show=False, branch_labels=lambda c: c.branch_length)
src/b/i/biopython-1.63/Tests/test_Phylo_depend.py biopython(Download)
dollo = Phylo.read(EX_DOLLO, 'phyloxml') apaf = Phylo.read(EX_APAF, 'phyloxml') Phylo.draw(dollo, do_show=False) Phylo.draw(apaf, do_show=False) # Fancier options Phylo.draw(apaf, do_show=False, branch_labels={apaf.root: 'Root'}) Phylo.draw(apaf, do_show=False, branch_labels=lambda c: c.branch_length)