Python Tree.show方法代码示例

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [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 Tree [as 别名]
# 或者: from ete3.Tree import show [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 Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
def draw_tree(tree_string):
    
    t = Tree(tree_string, format=8)
    
    def mylayout(node):
        #if node.name != 'L':
        file = 'tmp/%s.png' % node.name
        new_face = faces.ImgFace(file)
        new_face.rotable = True
        new_face.rotation = -90
        #new_face.margin_top = 50
        new_face.margin_left = 15
        faces.add_face_to_node(new_face, node, column=0 , position='branch-top')
        
    ts = TreeStyle()
    ts.rotation = 90
    ts.layout_fn = mylayout
    t.show(tree_style = ts)
    plt.clf()

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
I.aligned_foot.add_face( faces.TextFace("FO1"), 2 )
I.aligned_foot.add_face( faces.TextFace("F1"), 3 )
I.aligned_foot.add_face( faces.TextFace("FO1"), 4 )

I.legend.add_face(faces.CircleFace(30, random_color(), "sphere"), 0)
I.legend.add_face(faces.CircleFace(30, random_color(), "sphere"), 0)
I.legend.add_face(faces.TextFace("HOLA"), 1)
I.legend.add_face(faces.TextFace("HOLA"), 1)

# Creates a random tree with 10 leaves
t2 = Tree()
t2.populate(10)

# Creates a fixed NodeStyle object containing a TreeFace (A tree image
# as a face within another tree image)
# t.add_face(faces.TreeFace(t2, I), "branch-right", 0)

# Attach the fixed style to the first child of the root node
# t.children[0].img_style = style
I.rotation = 90
I.mode = "c"
t.show(tree_style=I)
#t.render("/home/jhuerta/test.svg", img_properties=I)
#t.render("/home/jhuerta/test.pdf", img_properties=I)
#t.render("/home/jhuerta/test.png", img_properties=I)
#t.render("/home/jhuerta/test.ps", img_properties=I)
#os.system("inkscape /home/jhuerta/test.svg")
#I.mode = "c"
#t.show(img_properties=I)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
    
    else:  # for child
        #### search the parent node by parent_id
        node_cur = root.search_nodes(name=str(parent_id))
        # there should be only one parent node
        if len(node_cur) == 1:
            #### set child with its id
            node_cur = node_cur[0].add_child(name=str(cell_id))  
            #### set duration
            node_cur.add_feature("dist", time_duration)
            
            # set node style
            node_cur.set_style(ns)
            
            # set node name to face
            nameFace = TextFace(node_cur.name)
            nameFace.fgcolor = "white"
            nameFace.fsize = 15
            nameFace.background.color = "green"
            node_cur.add_face(nameFace, column=1, position="branch-bottom")
        else:
            raise RuntimeError("the cell id should be unique!")
            
        
#node = root.search_nodes(name=str(5))
#node[0].add_feature("dist", 1.5)
    
print root.get_ascii()

root.show(tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
# for key in prune_count.keys():
#     # node_weight = ln(prune_count[key])
#     # node_weight = ln(n_children)
#     # print(node_weight,n_children)
#     # node = lookup[key]
#     node.add_features(weight=random.randint(50))

for n in t.traverse():
    n.add_face(TextFace(n.name, fsize = 16), column=0, position="branch-bottom")
    # n.add_features(weight=random.randint(0,20))

t.prune(prune_list)
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
# ts.mode = "c"  # this makes it circular
# False need to add node names manually
ts.show_leaf_name = False
ts.scale = 120

# Show branch data
ts.show_branch_length = False
ts.show_branch_support = True


# print (t.get_ascii(show_internal=True))

t.show(tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
                    if beginMSA == 'NA':
                        iesmotif.append([int(begin), int(end),"()", 10, 10, "red", "black", "arial|8|black|?"])
                    else:
                        iesmotif.append([int(begin), int(end),"()", 10, 10, "red", "black", "arial|8|black|?"])
                elif ies == '1':
                    iesmotif.append([int(beginMSA), int(endMSA),"[]", 10, 10, "black", "red", "arial|8|black|" + iesId])
                elif ies == '0':
                    iesmotif.append([int(begin), int(end), "[]", 10, 10, "silver", "silver", None])
                else:
                    quit(1)
            seqFace = SeqMotifFace(seq = seq, motifs = iesmotif, gap_format = "blank", seq_format = "line")
            leaf.add_face(seqFace, 0, "aligned")
        drawTree(outputFile)


    """
t.show()

# Draw trees.

pp = pprint.PrettyPrinter(indent=8)

# SPECIATION TREE #
###################
wgd1 = Tree('((P_caudatum:1[&&NHX:Ev=S:S=3:ND=3],(((P_sexaurelia:1[&&NHX:Ev=S:S=7:ND=7],P_sonneborni:1[&&NHX:Ev=S:S=8:ND=8]):1[&&NHX:Ev=S:S=5:ND=5],(((P_pentaurelia:1[&&NHX:Ev=S:S=13:ND=13],P_primaurelia:1[&&NHX:Ev=S:S=14:ND=14]):1[&&NHX:Ev=S:S=11:ND=11],(P_biaurelia:1[&&NHX:Ev=S:S=15:ND=15],(P_octaurelia:1[&&NHX:Ev=S:S=17:ND=17],P_tetraurelia:1[&&NHX:Ev=S:S=18:ND=18]):1[&&NHX:Ev=S:S=16:ND=16]):1[&&NHX:Ev=S:S=12:ND=12]):1[&&NHX:Ev=S:S=9:ND=9],P_tredecaurelia:1[&&NHX:Ev=S:S=10:ND=10]):1[&&NHX:Ev=S:S=6:ND=6]):1[&&NHX:Ev=S:S=4:ND=4],((P_sexaurelia:1[&&NHX:Ev=S:S=7:ND=7],P_sonneborni:1[&&NHX:Ev=S:S=8:ND=8]):1[&&NHX:Ev=S:S=5:ND=5],(((P_pentaurelia:1[&&NHX:Ev=S:S=13:ND=13],P_primaurelia:1[&&NHX:Ev=S:S=14:ND=14]):1[&&NHX:Ev=S:S=11:ND=11],(P_biaurelia:1[&&NHX:Ev=S:S=15:ND=15],(P_octaurelia:1[&&NHX:Ev=S:S=17:ND=17],P_tetraurelia:1[&&NHX:Ev=S:S=18:ND=18]):1[&&NHX:Ev=S:S=16:ND=16]):1[&&NHX:Ev=S:S=12:ND=12]):1[&&NHX:Ev=S:S=9:ND=9],P_tredecaurelia:1[&&NHX:Ev=S:S=10:ND=10]):1[&&NHX:Ev=S:S=6:ND=6]):1[&&NHX:Ev=S:S=4:ND=4]):1[&&NHX:Ev=D:S=4:ND=4]):1[&&NHX:Ev=S:S=1:ND=1],T_thermophila:1[&&NHX:Ev=S:S=2:ND=2])[&&NHX:Ev=S:S=0:ND=0];')

basest = Tree('((P_caudatum:1[&&NHX:Ev=S:S=3:ND=3],((P_sexaurelia:1[&&NHX:Ev=S:S=7:ND=7],P_sonneborni:1[&&NHX:Ev=S:S=8:ND=8]):1[&&NHX:Ev=S:S=5:ND=5],(((P_pentaurelia:1[&&NHX:Ev=S:S=13:ND=13],P_primaurelia:1[&&NHX:Ev=S:S=14:ND=14]):1[&&NHX:Ev=S:S=11:ND=11],(P_biaurelia:1[&&NHX:Ev=S:S=15:ND=15],(P_octaurelia:1[&&NHX:Ev=S:S=17:ND=17],P_tetraurelia:1[&&NHX:Ev=S:S=18:ND=18]):1[&&NHX:Ev=S:S=16:ND=16]):1[&&NHX:Ev=S:S=12:ND=12]):1[&&NHX:Ev=S:S=9:ND=9],P_tredecaurelia:1[&&NHX:Ev=S:S=10:ND=10]):1[&&NHX:Ev=S:S=6:ND=6]):1[&&NHX:Ev=S:S=4:ND=4]):1[&&NHX:Ev=S:S=1:ND=1],T_thermophila:1[&&NHX:Ev=S:S=2:ND=2])[&&NHX:Ev=S:S=0:ND=0];')

colorNodes(wgd1, 0)
ts = TreeStyle()
#ts.show_leaf_name = False

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
import sys
from ete3 import Tree
import ete3 #for good error messages
import six.moves.cPickle as pickle

'''
	python 2. 7 program
	input your tree on command line in double quotes!
'''

try:
	newick_trees = sys.argv[1:]
except:
	print "There were errors in parsing the command line!"
	sys.exit(1)

try:
	for tree_string in newick_trees:
		t = Tree(tree_string)
		t.show()
except ete3.parser.newick.NewickError, e:
	print "invalid newick tree:", e

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
def run(args):
    if args.text_mode:
        from ete3 import Tree
        for tindex, tfile in enumerate(args.src_tree_iterator):
            #print tfile
            if args.raxml:
                nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
                t = Tree(nw)
            else:
                t = Tree(tfile)

            print(t.get_ascii(show_internal=args.show_internal_names,
                              attributes=args.show_attributes))
        return

    import random
    import re
    import colorsys
    from collections import defaultdict
    from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
                         add_face_to_node, random_color)

    global FACES

    if args.face:
        FACES = parse_faces(args.face)
    else:
        FACES = []

    # VISUALIZATION
    ts = TreeStyle()
    ts.mode = args.mode
    ts.show_leaf_name = True
    ts.tree_width = args.tree_width


    for f in FACES:
        if f["value"] == "@name":
            ts.show_leaf_name = False
            break

    if args.as_ncbi:
        ts.show_leaf_name = False
        FACES.extend(parse_faces(
            ['value:@sci_name, size:10, fstyle:italic',
             'value:@taxid, color:grey, size:6, format:" - %s"',
             'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
             'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
         ]))


    if args.alg:
        FACES.extend(parse_faces(
            ['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
         ))

    if args.heatmap:
        FACES.extend(parse_faces(
            ['value:@name, size:10, pos:aligned, ftype:heatmap']
         ))

    if args.bubbles:
        for bubble in args.bubbles:
            FACES.extend(parse_faces(
                ['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
             ]))

    ts.branch_vertical_margin = args.branch_separation
    if args.show_support:
        ts.show_branch_support = True
    if args.show_branch_length:
        ts.show_branch_length = True
    if args.force_topology:
        ts.force_topology = True
    ts.layout_fn = lambda x: None

    for tindex, tfile in enumerate(args.src_tree_iterator):
        #print tfile
        if args.raxml:
            nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
            t = PhyloTree(nw)
        else:
            t = PhyloTree(tfile)


        if args.alg:
            t.link_to_alignment(args.alg, alg_format=args.alg_format)

        if args.heatmap:
            DEFAULT_COLOR_SATURATION = 0.3
            BASE_LIGHTNESS = 0.7
            def gradient_color(value, max_value, saturation=0.5, hue=0.1):
                def rgb2hex(rgb):
                    return '#%02x%02x%02x' % rgb
                def hls2hex(h, l, s):
                    return rgb2hex( tuple([int(x*255) for x in colorsys.hls_to_rgb(h, l, s)]))

                lightness = 1 - (value * BASE_LIGHTNESS) / max_value
                return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)

#.........这里部分代码省略.........

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import show [as 别名]
        col = 0
        for i, name in enumerate(set(node.get_leaf_names())):
            if i>0 and i%2 == 0:
                col += 1
            # Add the corresponding face to the node
            if name.startswith("Dme"):
                faces.add_face_to_node(flyFace, node, column=col)
            elif name.startswith("Dre"):
                faces.add_face_to_node(fishFace, node, column=col)
            elif name.startswith("Mms"):
                faces.add_face_to_node(mouseFace, node, column=col)
            elif name.startswith("Ptr"):
                faces.add_face_to_node(chimpFace, node, column=col)
            elif name.startswith("Hsa"):
                faces.add_face_to_node(humanFace, node, column=col)
            elif name.startswith("Cfa"):
                faces.add_face_to_node(dogFace, node, column=col)

            # Modifies this node's style
            node.img_style["size"] = 16
            node.img_style["shape"] = "sphere"
            node.img_style["fgcolor"] = "#AA0000"

    # If leaf is "Hsa" (homo sapiens), highlight it using a
    # different background.
    if node.is_leaf() and node.name.startswith("Hsa"):
        node.img_style["bgcolor"] = "#9db0cf"

# And, finally, Visualize the tree using my own layout function
t.show(mylayout)