from ete_dev import Tree # Creates an empty tree and populates it with some new # nodes t = Tree() A = t.add_child(name="A") B = t.add_child(name="B") C = A.add_child(name="C") D = A.add_child(name="D") print t # /-C # /--------| #---------| \-D # | # \-B print 'is "t" the root?', t.is_root() # True print 'is "A" a terminal node?', A.is_leaf() # False print 'is "B" a terminal node?', B.is_leaf() # True print 'B.get_tree_root() is "t"?', B.get_tree_root() is t # True print 'Number of leaves in tree:', len(t) # returns number of leaves under node (3) print 'is C in tree?', C in t # Returns true print "All leaf names in tree:", [node.name for node in t]
from ete_dev import Tree
# Creates an empty tree and populates it with some new
# nodes
t = Tree()
A = t.add_child(name="A")
B = t.add_child(name="B")
C = A.add_child(name="C")
D = A.add_child(name="D")
print t
# /-C
# /--------|
#---------| \-D
# |
# \-B
print 'is "t" the root?', t.is_root() # True
print 'is "A" a terminal node?', A.is_leaf() # False
print 'is "B" a terminal node?', B.is_leaf() # True
print 'B.get_tree_root() is "t"?', B.get_tree_root() is t # True
print 'Number of leaves in tree:', len(
t) # returns number of leaves under node (3)
print 'is C in tree?', C in t # Returns true
print "All leaf names in tree:", [node.name for node in t]
from ete_dev import Tree, TreeStyle, NodeStyle, PhyloTree, faces from ete_dev.treeview.faces import * from ete_dev.treeview.main import random_color, _NODE_TYPE_CHECKER, FACE_POSITIONS sys.path.insert(0, os.path.join(ETEPATH, "examples/treeview")) import face_grid, bubble_map, item_faces, node_style, node_background, face_positions, face_rotation, seq_motif_faces, barchart_and_piechart_faces sys.path.insert(0, os.path.join(ETEPATH, "examples/phylogenies")) import phylotree_visualization main_tree = Tree() main_tree.dist = 0 t, ts = face_grid.get_example_tree() t_grid = TreeFace(t, ts) n = main_tree.add_child() n.add_face(t_grid, 0, "aligned") t, ts = bubble_map.get_example_tree() t_bubble = TreeFace(t, ts) n = main_tree.add_child() n.add_face(t_bubble, 0, "aligned") t, ts = item_faces.get_example_tree() t_items = TreeFace(t, ts) n = main_tree.add_child() n.add_face(t_items, 0, "aligned") t, ts = node_style.get_example_tree() t_nodest = TreeFace(t, ts) n = main_tree.add_child()
from ete_dev import Tree t = Tree() # Creates an empty tree A = t.add_child(name="A") # Adds a new child to the current tree root # and returns it B = t.add_child(name="B") # Adds a second child to the current tree # root and returns it C = A.add_child(name="C") # Adds a new child to one of the branches D = C.add_sister(name="D") # Adds a second child to same branch as # before, but using a sister as the starting # point R = A.add_child(name="R") # Adds a third child to the # branch. Multifurcations are supported # Next, I add 6 random leaves to the R branch names_library is an # optional argument. If no names are provided, they will be generated # randomly. R.populate(6, names_library=["r1", "r2", "r3", "r4", "r5", "r6"]) # Prints the tree topology print t # /-C # | # |--D # | # /--------| /-r4 # | | /--------| # | | /--------| \-r3 # | | | | # | | | \-r5 # | \--------| # ---------| | /-r6 # | | /--------| # | \--------| \-r2
ts = TreeStyle()
ts.mode = "c"
ts.arc_span = 360
ts.layout_fn = layout
ts.show_leaf_name = False
ts.show_border = True
ts.draw_guiding_lines = False
ts.show_scale = True
#ts.scale = 60
t = Tree()
t.dist = 0
t.size = 0, 0
for x in xrange(100):
n = t.add_child()
n = n.add_child()
n = n.add_child()
n2 = n.add_child()
n3 = n.add_child()
n4 = n2.add_child()
n5 = n3.add_child()
# n.size = (10, 10)
# n2.size = (10, 70)
# n3.size = (40, 40)
# n4.size = (10, 10)
#n2.size = 10
#n3.size = 10
#n5.size = 10
#n2.dist = 0.1
#n2.size = 1
ts = TreeStyle()
ts.mode = "c"
ts.arc_span = 360
ts.layout_fn = layout
ts.show_leaf_name = False
ts.show_border = True
ts.draw_guiding_lines = False
ts.show_scale = True
#ts.scale = 60
t = Tree()
t.dist = 0
t.size = 0,0
for x in xrange(100):
n = t.add_child()
n = n.add_child()
n = n.add_child()
n2 = n.add_child()
n3 = n.add_child()
n4 = n2.add_child()
n5 = n3.add_child()
# n.size = (10, 10)
# n2.size = (10, 70)
# n3.size = (40, 40)
# n4.size = (10, 10)
#n2.size = 10
#n3.size = 10
#n5.size = 10
#n2.dist = 0.1
#n2.size = 1
from ete_dev import Tree
t = Tree() # Creates an empty tree
A = t.add_child(name="A") # Adds a new child to the current tree root
# and returns it
B = t.add_child(name="B") # Adds a second child to the current tree
# root and returns it
C = A.add_child(name="C") # Adds a new child to one of the branches
D = C.add_sister(name="D") # Adds a second child to same branch as
# before, but using a sister as the starting
# point
R = A.add_child(name="R") # Adds a third child to the
# branch. Multifurcations are supported
# Next, I add 6 random leaves to the R branch names_library is an
# optional argument. If no names are provided, they will be generated
# randomly.
R.populate(6, names_library=["r1","r2","r3","r4","r5","r6"])
# Prints the tree topology
print t
# /-C
# |
# |--D
# |
# /--------| /-r4
# | | /--------|
# | | /--------| \-r3
# | | | |
# | | | \-r5
# | \--------|
# ---------| | /-r6
# | | /--------|
# | \--------| \-r2