import sys
import random
from ete2 import Tree, faces, TreeStyle, COLOR_SCHEMES
schema_names = COLOR_SCHEMES.keys()
def layout(node):
if node.is_leaf():
F= faces.PieChartFace([10,10,10,10,10,10,10,10,10,4,6],
colors=COLOR_SCHEMES["set3"],
width=50, height=50)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F,node, 0, position="branch-right")
F= faces.PieChartFace([10,20,5,5,60],
colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]],
width=100, height=40)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F,node, 0, position="branch-right")
else:
F= faces.BarChartFace([40,20,70,100,30,40,50,40,70,-12], min_value=-12,
colors=COLOR_SCHEMES["spectral"],
labels = "aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","),
label_fsize=10, scale_fsize=10)
faces.add_face_to_node(F,node, 0, position="branch-top")
F.background.color = "#eee"
def get_example_tree():
t = Tree()
def main(argv):
input_file=''
title='Title'
label_internal_nodes = False
label_leaves = False
out_file=''
width=750
out_file_xml=''
try:
opts, args = getopt.getopt(argv,"h:i:t:lno:w:x:",["Help=","InputFile=","Title=","LabelLeaves=", "LabelInternalNodes=","OutFile=","Width=","OutFileXML="])
except getopt.GetoptError:
print 'Unknown option, call using: ./PlotTree.py -i <InputCAMIFile> -t <Title> -l <LabelLeavesFlag> -n <LabelInternalNodesFlag> -o <OutFile.png> -x <Outfile.xml> -w <Width>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print './PlotTree.py -i <InputCAMIFile> -t <Title> -l <LabelLeavesFlag> -n <LabelInternalNodesFlag> -o <OutFile> -x <OutFile.xml> -w <Width>'
sys.exit(2)
elif opt in ("-i", "--InputFile"):
input_file = arg
elif opt in ("-t", "--Title"):
title = arg
elif opt in ("-l", "--LabelLeaves"):
label_leaves = True
elif opt in ("-n","--LabelInternalNodes"):
label_internal_nodes = True
elif opt in ("-o", "--OutFile"):
out_file = arg
elif opt in ("-w", "--Width"):
width = int(arg)
elif opt in ("-x", "--OutFileXML"):
out_file_xml = arg
schema_names = COLOR_SCHEMES.keys()
#Read the common kmer profile
ckm_tax_paths = []
ckm_name_to_perc = dict()
fid = open(input_file,'r')
file = fid.readlines()
fid.close()
#Put placeholders in for missing names like: "||" -> "|NA1|"
file_noblank = list()
i=0
for line in file:
while "||" in line:
line = line.replace("||","|NONAME|",1)
i = i+1
file_noblank.append(line)
#Get the names and weights
for line in file_noblank:
if line[0]!='#' and line[0]!='@' and line[0]!='\n': #Don't parse comments or blank lines
temp = line.split()[3] #Get the names
ckm_tax_paths.append(temp)
ckm_name_to_perc[temp.split("|")[-1]] = line.split()[-1] #Get the weights
#Create the tree
t=Tree()
names_to_nodes = dict()
for i in range(0,len(ckm_tax_paths)):
split_tax_path = ckm_tax_paths[i].split("|")
if len(split_tax_path)==1: #If len==1, then it's a superkingdom
names_to_nodes[split_tax_path[0]] = t.add_child(name=split_tax_path[0]) #connect directly to tree
else:
if split_tax_path[-2] in names_to_nodes: #If the parent is already in the tree, add to tree
names_to_nodes[split_tax_path[-1]] = names_to_nodes[split_tax_path[-2]].add_child(name=split_tax_path[-1])
else: #Otherwise iterate up until we have something that is in the tree
j=2
while split_tax_path[-j]=="NONAME":
j = j + 1
#This skips over the NONAMES
names_to_nodes[split_tax_path[-1]] = names_to_nodes[split_tax_path[-j]].add_child(name=split_tax_path[-1])
#Show the tree
#print t.get_ascii(show_internal=True)
#scheme = random.sample(schema_names, 1)[0] #'set2' is nice,
scheme = 'set2'
def layout(node):
if node.name in ckm_name_to_perc:
ckm_perc = float(ckm_name_to_perc[node.name])
else:
ckm_perc = 0
F = CircleFace(radius=3.14*math.sqrt(ckm_perc), color="RoyalBlue", style="sphere")
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="branch-right")
if label_internal_nodes:
faces.add_face_to_node(TextFace(node.name, fsize=7),node, 0, position="branch-top")
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = label_leaves
ts.min_leaf_separation = 50
ts.title.add_face(TextFace(title, fsize=20), column=0)
#Export the tree to a png image
t.render(out_file, w=width, units="mm", tree_style=ts)
#Export the xml file
project = Phyloxml()
phylo = phyloxml.PhyloxmlTree(newick=t.write(format=0, features=[]))
phylo.phyloxml_phylogeny.set_name(title)
project.add_phylogeny(phylo)
project.export(open(out_file_xml,'w'))