t = get_example_tree(File)
#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)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-t",
action="store",
dest="treef",
help="The tree file")
parser.add_argument("-s",
action="store",
dest="statf",
help="The statistics file")
parser.add_argument("-c",
action="store",
default=0,
type=float,
dest="scaling",
help="If this parameter is set "
"to more than 0, "
"the size of the pie charts "
"correlate with the total "
"number of events at a node "
"(and are scaled by the factor "
"given as a float).")
parser.add_argument(
"-e",
action="store",
type=str,
default="all",
dest="event",
help=
"If an event type is specified, just this event type is visualized. Per default all event types are shown on the tree.\n"
"all\n"
"fusions\n"
"fissions\n"
"termLosses\n"
"termEmergences\n"
"singleDomainLosses\n"
"singleDomainEmergences")
parser.add_argument(
"-p",
action="store",
dest="treeshape",
default="r",
choices=["c", "r"],
help="shape of the tree, circle (c) or tree format (r)")
parser.add_argument("-o", action="store", dest="outputname")
parser.add_argument(
"-y",
action="store",
type=str,
dest="NodeIDtreeName",
default=None,
help="Name for output file that shows a tree with all node IDs.")
parser.add_argument(
"-l",
dest="short_legend",
help=
"Writes the full legend for all events in two levels for short trees",
action="store_true")
params = parser.parse_args()
if (params.event not in ("all", "fusions", "fissions", "termLosses",
"termEmergences", "singleDomainLosses",
"singleDomainEmergences")):
print(
"Error: Please specify a valid event type. For a list of possible options use the --help parameter."
)
sys.exit(1)
if params.NodeIDtreeName != None:
id_tree = Tree(params.treef, format=0)
coun = 0
for node in id_tree.traverse('preorder'):
node.add_features(ID=coun)
coun += 1
# Create empty TreeStyle
ts = TreeStyle()
# Set custom layout function
ts.layout_fn = layout_idtree
# Draw tree
ts.mode = params.treeshape
ts.complete_branch_lines_when_necessary = True
ts.extra_branch_line_type = 0
ts.extra_branch_line_color = "black"
# ts.optimal_scale_level ="full"
ts.branch_vertical_margin = 40
ts.scale = 100
# We will add node names manually
ts.show_leaf_name = False
ts.draw_guiding_lines = True
if (params.NodeIDtreeName.endswith(".pdf")):
pathout = params.NodeIDtreeName
else:
pathout = params.NodeIDtreeName + ".pdf"
id_tree.render(pathout, dpi=1200, tree_style=ts)
pl.close()
else:
tree = Tree(params.treef, format=0)
# Read statistics file
node_stat_dict = {}
with open(params.statf, "r") as sf:
for line in sf:
# Stop the loop at the second part of statistics file
if line.startswith(
"# Number of events per domain."
) or line.startswith(
"# Events per domain arrangement for last common ancestor"
):
break
if line[0] not in ('#', '\n'):
vecline = line.strip().split()
id = vecline.pop(0)
stats = [int(i) for i in vecline]
node_stat_dict[int(id)] = stats
# determine max. number of events per node for scaling
fus_max = 0
fis_max = 0
termLoss_max = 0
termGain_max = 0
singLoss_max = 0
singGain_max = 0
tot_max = 0
# Assign rearrangement events to leaves
c = 0
for node in tree.traverse('preorder'):
node.add_features(fusion=node_stat_dict[c][0])
if (node_stat_dict[c][0] > fus_max):
fus_max = node_stat_dict[c][0]
node.add_features(fission=node_stat_dict[c][1])
if (node_stat_dict[c][1] > fis_max):
fis_max = node_stat_dict[c][1]
node.add_features(termLoss=node_stat_dict[c][2])
if (node_stat_dict[c][2] > termLoss_max):
termLoss_max = node_stat_dict[c][2]
node.add_features(termGain=node_stat_dict[c][3])
if (node_stat_dict[c][3] > termGain_max):
termGain_max = node_stat_dict[c][3]
node.add_features(singLoss=node_stat_dict[c][4])
if (node_stat_dict[c][4] > singLoss_max):
singLoss_max = node_stat_dict[c][4]
node.add_features(singGain=node_stat_dict[c][5])
if (node_stat_dict[c][5] > singGain_max):
singGain_max = node_stat_dict[c][5]
if (sum(node_stat_dict[c]) > tot_max):
tot_max = sum(node_stat_dict[c])
c += 1
global scal
scal = params.scaling
global eve
event_options = {
"all": 0,
"fusions": 1,
"fissions": 2,
"termLosses": 3,
"termEmergences": 4,
"singleDomainLosses": 5,
"singleDomainEmergences": 6
}
eve = event_options[params.event]
# Create empty TreeStyle
ts = TreeStyle()
# Set custom layout function
ts.layout_fn = layout_gen_events
# Draw tree
ts.mode = params.treeshape
ts.complete_branch_lines_when_necessary = True
ts.extra_branch_line_type = 0
ts.extra_branch_line_color = "black"
#ts.optimal_scale_level ="full"
ts.branch_vertical_margin = 40
ts.scale = 100
# We will add node names manually
ts.show_leaf_name = False
# legend creation
if (params.event == "all"):
ts.legend.add_face(CircleFace(10, "DimGray"), column=0)
ts.legend.add_face(TextFace(" Fusion ",
fsize=16,
fgcolor='DimGray'),
column=1)
ts.legend.add_face(CircleFace(10, "DeepPink"), column=2)
ts.legend.add_face(TextFace(' Fission ',
fsize=16,
fgcolor='DeepPink'),
column=3)
ts.legend.add_face(CircleFace(10, "YellowGreen"), column=4)
ts.legend.add_face(TextFace(' Terminal Loss ',
fsize=16,
fgcolor='YellowGreen'),
column=5)
if params.short_legend:
ts.legend.add_face(CircleFace(10, "DarkBlue"), column=0)
ts.legend.add_face(TextFace(' Terminal Emergence ',
fsize=16,
fgcolor='DarkBlue'),
column=1)
ts.legend.add_face(CircleFace(10, "Chocolate"), column=2)
ts.legend.add_face(TextFace(' Single Domain Loss ',
fsize=16,
fgcolor='Chocolate'),
column=3)
ts.legend.add_face(CircleFace(10, "DeepSkyBlue"), column=4)
ts.legend.add_face(TextFace(' Single Domain Emergence ',
fsize=16,
fgcolor='DeepSkyBlue'),
column=5)
else:
ts.legend.add_face(CircleFace(10, "DarkBlue"), column=6)
ts.legend.add_face(TextFace(' Terminal Emergence ',
fsize=16,
fgcolor='DarkBlue'),
column=7)
ts.legend.add_face(CircleFace(10, "Chocolate"), column=8)
ts.legend.add_face(TextFace(' Single Domain Loss ',
fsize=16,
fgcolor='Chocolate'),
column=9)
ts.legend.add_face(CircleFace(10, "DeepSkyBlue"), column=10)
ts.legend.add_face(TextFace(' Single Domain Emergence ',
fsize=16,
fgcolor='DeepSkyBlue'),
column=11)
elif (params.event == "fusions"):
ts.legend.add_face(CircleFace(10, "DimGray"), column=0)
ts.legend.add_face(TextFace(" Fusion ",
fsize=16,
fgcolor='DimGray'),
column=1)
elif (params.event == "fissions"):
ts.legend.add_face(CircleFace(10, "DeepPink"), column=0)
ts.legend.add_face(TextFace(' Fission ',
fsize=16,
fgcolor='DeepPink'),
column=1)
elif (params.event == "termLosses"):
ts.legend.add_face(CircleFace(10, "YellowGreen"), column=0)
ts.legend.add_face(TextFace(' Terminal Loss ',
fsize=16,
fgcolor='YellowGreen'),
column=1)
elif (params.event == "termEmergences"):
ts.legend.add_face(CircleFace(10, "DarkBlue"), column=0)
ts.legend.add_face(TextFace(' Terminal Emergence ',
fsize=16,
fgcolor='DarkBlue'),
column=1)
elif (params.event == "singleDomainLosses"):
ts.legend.add_face(CircleFace(10, "Chocolate"), column=0)
ts.legend.add_face(TextFace(' Single Domain Loss ',
fsize=16,
fgcolor='Chocolate'),
column=1)
elif (params.event == "singleDomainEmergences"):
ts.legend.add_face(CircleFace(10, "DeepSkyBlue"), column=0)
ts.legend.add_face(TextFace(' Single Domain Emergence ',
fsize=16,
fgcolor='DeepSkyBlue'),
column=1)
ts.legend_position = 1
ts.draw_guiding_lines = True
if (params.outputname.endswith(".pdf")):
pathout = params.outputname
else:
pathout = params.outputname + ".pdf"
tree.render(pathout, dpi=1200, tree_style=ts)
pl.close()
sys.exit(0)
n.add_features(S=Res_dict[str(i)]["S"])
i += 1
sp_t.write(format=1,
features=["D", "S"],
outfile=args.o + ".nhx",
format_root_node=True)
if os.environ.has_key("DISPLAY"):
from ete3 import TreeStyle, TextFace
# Basic tree style
tree_style = TreeStyle()
tree_style.show_leaf_name = False
tree_style.show_branch_length = False
tree_style.show_scale = False
tree_style.extra_branch_line_type = 0 # 0=solid, 1=dashed, 2=dotted
tree_style.extra_branch_line_color = "black"
i = 0
for n in sp_t.traverse():
n.dist = 5
Dstrinq = " D: " + str(Res_dict[str(i)]["D"])
Sstrinq = " S: " + str(Res_dict[str(i)]["S"])
n.add_face(TextFace(Dstrinq, fgcolor="#1C01AC"),
column=0,
position='branch-bottom')
n.add_face(TextFace(Sstrinq, fgcolor="#800080"),
column=0,
position='branch-bottom')
if n.is_leaf():
n.add_face(TextFace(
