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 = 0
ts.guiding_lines_color = "#000000"
self._treestyle = ts
return ts
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
default="pies.svg")
args = parser.parse_args()
plot_tree, subtrees_dict, subtrees_topids = get_phyparts_nodes(
args.species_tree, args.phyparts_root)
concord_dict, conflict_dict = get_concord_and_conflict(args.phyparts_root,
subtrees_dict,
subtrees_topids)
phyparts_dist, phyparts_pies = get_pie_chart_data(args.phyparts_root,
args.num_genes, concord_dict,
conflict_dict)
#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
n.set_style(nstyle)
n.img_style["vt_line_width"] = 0
ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
my_svg = plot_tree.render(args.svg_name, tree_style=ts, w=595)
from ete3 import TreeStyle
from ete3 import EvolTree
from ete3 import faces
tree = EvolTree("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta')
print(tree)
print('\n Running free-ratio model with calculation of ancestral sequences...')
tree.run_model('fb_anc')
#tree.link_to_evol_model('/tmp/ete3-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(
faces.TextFace('node_id: #%d ' % (n.node_id), fsize=8), 0)
print('display result of bs_anc model, with ancestral amino acid sequences.')
tree.show(tree_style=I)
print('\nThe End.')
F = faces.TextFace(mynode.name,fsize=20)
faces.add_face_to_node(F,mynode,0,position="aligned")
#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
n.set_style(nstyle)
n.img_style["vt_line_width"] = 0
ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
plot_tree.ladderize(direction=1)
my_svg = plot_tree.render(args.svg_name,tree_style=ts,w=595,dpi=300)
if args.show_nodes:
node_style = TreeStyle()
node_style.show_leaf_name=False
node_style.layout_fn = node_text_layout
plot_tree.show(tree_style=node_style)
#выбор стиля
circular_style = TreeStyle()
circular_style.show_leaf_name = False
circular_style.show_branch_length = True
circular_style.show_branch_support = True
circular_style.scale = 75
circular_style.tree_width = 50
#circular_style.rotation = 90
#circular_style.extra_branch_line_type=(0)
#circular_style.guiding_lines_type= (0)
#circular_style.title.add_face(TextFace(File, fsize=25), column=0)
circular_style.layout_fn = layout
t.render(adres+"/out/"+File[:-4]+".png", tree_style=circular_style)
circular_style.mode = "r" # draw tree in circular mode
circular_style.extra_branch_line_type=(2)
circular_style.guiding_lines_type= (2)
circular_style.guiding_lines_color =("red")
for n in t.traverse():
nstyle = NodeStyle()
nstyle["fgcolor"] = "red"
nstyle["size"] = 15
n.set_style(nstyle)
#N = AttrFace("name", fsize=30)
#faces.add_face_to_node(N, node, 0, position="aligned")
circular_style.legend.add_face =(TextFace("0.5 support"), column=1)
circular_style.legend.add_face =(CircleFace(10, "red"), column=0)
circular_style.layout_fn = layout
circular_style.legend.add_face(TextFace("0.5 support"), column=1)
circular_style.title.add_face(TextFace(File, fsize=40), column=0)
TextFace_=TextFace(text, ftype='Verdana', fsize=10, fgcolor='black', penwidth=0, fstyle='normal', tight_text=False, bold=False)
t.render(adres+"/out/"+File[:-4]+"_c.png", tree_style=circular_style)
from ete3 import faces
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print '\n Running free-ratio model with calculation of ancestral sequences...'
tree.run_model ('fb_anc')
#tree.link_to_evol_model('/tmp/ete3-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted (tree.get_descendants()+[tree],
key=lambda x: x.node_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace (n.sequence, 'aa', fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(faces.TextFace('node_id: #%d '%(n.node_id),
fsize=8), 0)
print 'display result of bs_anc model, with ancestral amino acid sequences.'
tree.show(tree_style=I)
print '\nThe End.'
