Python TreeStyle.layout_fn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 layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [as 别名]
def createImg(filename, thres=0, samples=1):
    count = parseLineage(filename)
    suffix, matrix, taxo = getSuffixandMatrixandNewick(count,thres,samples)
    newick = convert(taxo,suffix)
    newick += ';'

    t = Tree(newick, format=1)
    ct = ClusterTree(t.write(),  text_array=matrix)
    addColors(ct)

    # nodes are linked to the array table
    array = ct.arraytable
    # Calculates some stats on the matrix. Needed to establish the color gradients.
    matrix_dist = [i for r in xrange(len(array.matrix))for i in array.matrix[r] if np.isfinite(i)]
    matrix_max = np.max(matrix_dist)
    matrix_min = np.min(matrix_dist)
    matrix_avg = (matrix_max+matrix_min)/2
    # Creates a profile face that will represent node's profile as a heatmap
    profileFace  = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 14, "heatmap",colorscheme=3)
    # Creates my own layout function that uses previous faces
    def mylayout(node):
        # If node is a leaf
        if node.is_leaf():
            # And a line profile
            add_face_to_node(profileFace, node, 0, aligned=True)
            node.img_style["size"]=2

    # Use my layout to visualize the tree
    ts = TreeStyle()
    ts.layout_fn = mylayout
    # ct.show(tree_style=ts)
    filedir = '/'.join(filename.split('/')[:-1])
    # t.write(format=9, outfile="output/newick/"+param+".nw")
    ct.render(filedir+'/phylo.png',tree_style=ts)

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

    t = Tree()
    t.populate(8, reuse_names=False)

    ts = TreeStyle()
    ts.layout_fn = master_ly
    ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
    return t, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [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 layout_fn [as 别名]
def get_example_tree():
    # Create a random tree and add to each leaf a random set of motifs
    # from the original set
    t = Tree()
    t.populate(10)
    # for l in t.iter_leaves():
    #     seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))

    #     seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
    #                            seqtail_format="compactseq", scale_factor=1)
    #     seqFace.margin_bottom = 4
    #     f = l.add_face(seqFace, 0, "aligned")

    ts = TreeStyle()
    ts.layout_fn = layout
    return t, ts