Python TreeStyle.show_leaf_name方法代码示例

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():

    # Set dashed blue lines in all leaves
    nst1 = NodeStyle()
    nst1["bgcolor"] = "LightSteelBlue"
    nst2 = NodeStyle()
    nst2["bgcolor"] = "Moccasin"
    nst3 = NodeStyle()
    nst3["bgcolor"] = "DarkSeaGreen"
    nst4 = NodeStyle()
    nst4["bgcolor"] = "Khaki"


    t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
    for n in t.traverse():
        n.dist = 0

    n1 = t.get_common_ancestor("a1", "a2", "a3")
    n1.set_style(nst1)
    n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
    n2.set_style(nst2)
    n3 = t.get_common_ancestor("c1", "c2", "c3")
    n3.set_style(nst3)
    n4 = t.get_common_ancestor("b3", "b4")
    n4.set_style(nst4)
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    ts.mode = "c"
    ts.root_opening_factor = 1
    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():
    # Random tree
    t = Tree()
    t.populate(20, random_branches=True)

    # Some random features in all nodes
    for n in t.traverse():
        n.add_features(weight=random.randint(0, 50))

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    ts.layout_fn = layout

    # Draw a tree
    ts.mode = "c"

    # We will add node names manually
    ts.show_leaf_name = False
    # Show branch data
    ts.show_branch_length = True
    ts.show_branch_support = True

    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
    def ete_draw(self, fname=None):
        """ Draws the tree and saves it to a file.  If `fname` is None,
            show the tree instead of saving it.

            Args:
                fname: filename to save to (default=None)
        """
        if Cfg.USE_ETE3:
            def layout(node):
                faces.add_face_to_node(AttrFace("name"), node, column=0,
                                       position="branch-right")

            ts = TreeStyle()
            ts.show_leaf_name = False
            ts.layout_fn = layout
            ts.rotation = 90
            
            tree = EteTree(self.ete_str(), format=8)

            if fname:
                tree.render(fname, tree_style=ts)
            else:
                tree.show(tree_style=ts)
        else:
            # TODO maybe throw an error?
            pass

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "r"
    ts.show_leaf_name = False
    t.populate(10)
    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
 def get_tree_style(self):
     ts = TreeStyle()
     ts.layout_fn = self.custom_layout
     ts.show_leaf_name = False
     ts.draw_guiding_lines = True
     #ts.guiding_lines_type = 1
     self._treestyle = ts
     return ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():
    t = Tree()
    t.populate(10)
    ts = TreeStyle()
    ts.rotation = 45
    ts.show_leaf_name = False
    ts.layout_fn = rotation_layout

    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def export_tree(tree, filename, insignif_color, signif_color, i_group, width):
    '''
    exports the given tree to the given filename
    '''
    ts = TreeStyle()
    ts.show_leaf_name = False
    ts.show_scale = False
    ts.layout_fn = generate_layout(insignif_color, signif_color, i_group)
    tree.render(filename, w=width, tree_style=ts)

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "c"
    ts.show_leaf_name = True
    ts.min_leaf_separation = 15
    t.populate(100)
    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def balanceplot(balances, tree,
                layout=None,
                mode='c'):
    """ Plots balances on tree.

    Parameters
    ----------
    balances : np.array
        A vector of internal nodes and their associated real-valued balances.
        The order of the balances will be assumed to be in level order.
    tree : skbio.TreeNode
        A strictly bifurcating tree defining a hierarchical relationship
        between all of the features within `table`.
    layout : function, optional
        A layout for formatting the tree visualization. Must take a
        `ete.tree` as a parameter.
    mode : str
        Type of display to show the tree. ('c': circular, 'r': rectangular).

    Note
    ----
    The `tree` is assumed to strictly bifurcating and
    whose tips match `balances.

    See Also
    --------
    TreeNode.levelorder
    """
    # The names aren't preserved - let's pray that the topology is consistent.
    ete_tree = Tree(str(tree))
    # Some random features in all nodes
    i = 0
    for n in ete_tree.traverse():
        if not n.is_leaf():
            n.add_features(weight=balances[-i])
            i += 1

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    if layout is None:
        ts.layout_fn = default_layout
    else:
        ts.layout_fn = layout
    # Draw a tree
    ts.mode = mode

    # We will add node names manually
    ts.show_leaf_name = False
    # Show branch data
    ts.show_branch_length = True
    ts.show_branch_support = True

    return ete_tree, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_example_tree():

    t = Tree()
    t.populate(8)

    # Node style handling is no longer limited to layout functions. You
    # can now create fixed node styles and use them many times, save them
    # or even add them to nodes before drawing (this allows to save and
    # reproduce an tree image design)

    # Set bold red branch to the root node
    style = NodeStyle()
    style["fgcolor"] = "#0f0f0f"
    style["size"] = 0
    style["vt_line_color"] = "#ff0000"
    style["hz_line_color"] = "#ff0000"
    style["vt_line_width"] = 8
    style["hz_line_width"] = 8
    style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
    style["hz_line_type"] = 0
    t.set_style(style)

    #Set dotted red lines to the first two branches
    style1 = NodeStyle()
    style1["fgcolor"] = "#0f0f0f"
    style1["size"] = 0
    style1["vt_line_color"] = "#ff0000"
    style1["hz_line_color"] = "#ff0000"
    style1["vt_line_width"] = 2
    style1["hz_line_width"] = 2
    style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
    style1["hz_line_type"] = 2
    t.children[0].img_style = style1
    t.children[1].img_style = style1

    # Set dashed blue lines in all leaves
    style2 = NodeStyle()
    style2["fgcolor"] = "#000000"
    style2["shape"] = "circle"
    style2["vt_line_color"] = "#0000aa"
    style2["hz_line_color"] = "#0000aa"
    style2["vt_line_width"] = 2
    style2["hz_line_width"] = 2
    style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
    style2["hz_line_type"] = 1
    for l in t.iter_leaves():
        l.img_style = style2

    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def drawTree(treeFile, ShowBool):
	"""
	Draw a tree from a phy file
	"""
	t = Tree(treeFile)
	imgFile = treeFile.replace(".tree", ".tree.png")

	# Basic tree style
	ts = TreeStyle()
	ts.show_leaf_name = True
	ts.show_branch_support = True
	ts.scale =  160

	# Draws nodes as small red spheres of diameter equal to 10 pixels
	nstyle = NodeStyle()
	nstyle["shape"] = "sphere"
	nstyle["size"] = 10
	nstyle["fgcolor"] = "darkred"
	#nstyle["faces_bgcolor"] = "pink"

	nstyle2 = NodeStyle()
	nstyle2["shape"] = "sphere"
	nstyle2["size"] = 10
	nstyle2["fgcolor"] = "darkblue"
	


	# Gray dashed branch lines
	nstyle["hz_line_type"] = 1
	nstyle["hz_line_color"] = "#cccccc"

	# Applies the same static style to all nodes in the tree. Note that,
	# if "nstyle" is modified, changes will affect to all nodes
	for n in t.traverse():
		if n.is_leaf():
			if n.name.split("|")[-1] == "GI":
				n.set_style(nstyle)
			if n.name.split("|")[-1] == "plasmid":
				n.set_style(nstyle2)
			gi = n.name.split("|")[1]
			n.name = n.name.split("|")[0] #+ "   " + n.name.split("|")[1]
			n.name = n.name.replace("_tRNA_modification_GTPase_", "")
			n.name = n.name.replace("_DNA", "")
			n.name = " " + n.name + " "
			if n.name[-1] == "_": n.name.rstrip()
			
			taxon, color = taxonToColour(gi)
			n.add_face(TextFace(taxon, fgcolor = color, fsize = 8), column=1, position="branch-right")
			#n.img_style["bgcolor"] = color
			
	if ShowBool == True: #permet de flipper les braches pour avoir des topologies similaires
		t.show(tree_style=ts)
	t.render(imgFile, w=393, units="mm", tree_style=ts)

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def _get_motif_tree(tree, data, circle=True, vmin=None, vmax=None):
    try:
        from ete3 import Tree, NodeStyle, TreeStyle
    except ImportError:
        print("Please install ete3 to use this functionality")
        sys.exit(1)

    t = Tree(tree)
    
    # Determine cutoff for color scale
    if not(vmin and vmax):
        for i in range(90, 101):
            minmax = np.percentile(data.values, i)
            if minmax > 0:
                break
    if not vmin:
        vmin = -minmax
    if not vmax:
        vmax = minmax
    
    norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
    mapper = cm.ScalarMappable(norm=norm, cmap="RdBu_r")
    
    m = 25 / data.values.max()
    
    for node in t.traverse("levelorder"):
        val = data[[l.name for l in node.get_leaves()]].values.mean()
        style = NodeStyle()
        style["size"] = 0
        
        style["hz_line_color"] = to_hex(mapper.to_rgba(val))
        style["vt_line_color"] = to_hex(mapper.to_rgba(val))
        
        v = max(np.abs(m * val), 5)
        style["vt_line_width"] = v
        style["hz_line_width"] = v

        node.set_style(style)
    
    ts = TreeStyle()

    ts.layout_fn = _tree_layout
    ts.show_leaf_name= False
    ts.show_scale = False
    ts.branch_vertical_margin = 10

    if circle:
        ts.mode = "c"
        ts.arc_start = 180 # 0 degrees = 3 o'clock
        ts.arc_span = 180
    
    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
 def run_action_change_style(self, tree, a_data):
     #print "action change style called.."        
     if tree.tree_style == self._treestyle:
        ts2 = TreeStyle()
        ts2.layout_fn = self.custom_layout
        ts2.show_leaf_name = False
        ts2.draw_guiding_lines = True
        ts2.guiding_lines_type = 0 #solid line
        ts2.guiding_lines_color = a_data
        tree.tree_style = ts2
        self._treestyle = ts2
     else:
        tree.tree_style = self._treestyle

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def argument(name):
    g.name = name
    argument_file = "static/inputs/%s.txt" % name
    g.argument_tree = "/static/outputs/%s.png" % name
    argument_tree = "static/outputs/%s.png" % name

    try:
        f = open(argument_file)  # open the file
    except:
        abort(404)

    g.premises = []
    g.conclusion = None

    for line in f:
        g.premises.append(line.strip())
    g.conclusion = g.premises[-1]
    g.premises = g.premises[:-1]

    stmt_set = main.open_argument(argument_file)
    print stmt_set
    g.sat, tree = satisfiable.satisfiable(stmt_set)

    existing = os.listdir("static/outputs")
    for f in existing:
        if f == name + ".png":
            return render_template("argument.html")

    # set teh tree style...
    ts = TreeStyle()
    # don't show the name of the leaf nodes (which are just a x/o for a open/closed branch) in the final graph
    ts.show_leaf_name = False

    for child in tree.traverse():
        # add a marker with the name of each node, at each node
        child.add_face(TextFace(child.name), column=0, position="branch-top")

    # render the file and save it
    tree.render(argument_tree, tree_style=ts, w=5000)

    # crop out the unwanted part of the image...
    im = Image.open(argument_tree)
    (x, y) = im.size

    draw = ImageDraw.Draw(im)
    draw.rectangle((0, y*.5, x*.25, y), fill="white")
    im.save(argument_tree, "PNG")

    return render_template("argument.html")

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_leaf_name [as 别名]
def get_tree_style():
    ts = TreeStyle()
    # ts.mode = 'c'
    ts.margin_top = 10
    ts.margin_bottom = 10
    ts.margin_left = 10
    ts.margin_right = 10
    ts.show_leaf_name = False
    ts.show_branch_length = False
    ts.show_branch_support = False
    ts.show_scale = False
    title = TextFace("     Tax Assignment Tree", fsize=10)
    title.hz_align = 2
    title.vt_align = 2
    ts.title.add_face(TextFace(" "), column=0)
    ts.title.add_face(TextFace(" "), column=0)
    ts.title.add_face(title, column=0)
    return ts