def mktreeNode(self, tuples):
t = Tree()
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 10
nstyle["fgcolor"] = "darkred"
# Gray dashed branch lines
nstyle["hz_line_type"] = 1
nstyle["hz_line_color"] = "#cccccc"
t.set_style(nstyle)
if len(tuples) == 1:
t.name = '(' + tuples[0][0] + ',' + tuples[0][1] + ')'
else:
t.name = ""
return t
if len(args) < 1:
parser.error("incorrect number of arguments")
outfile_name = args[0]
path_to_draw_map_task = args[1]
lineage_files = args[2:]
def print_recursive( id, tree ):
print id
print tree[id]
for child in tree[id]['children'].keys():
print_recursive( child, tree )
tree = {}
tree_phylogeny = Tree()
ts = TreeStyle()
ts.show_leaf_name = False
ts.branch_vertical_margin = 10
#ts.scale = .1
def getNodeStyle( dictionary ):
aStyle = NodeStyle()
for key in dictionary.keys():
aStyle[key] = dictionary[key]
return aStyle
## node styles
for name in names:
if is_arabidopsis(name):
for n in tree.get_leaves_by_name(name):
nstyle = NodeStyle()
nstyle["bgcolor"] = 'red'
n.set_style(nstyle)
else:
for n in tree.get_leaves_by_name(name):
nstyle = NodeStyle()
nstyle["bgcolor"] = colour
n.set_style(nstyle)
#t = PhyloTree("RAxML_result.ITPR_LIKE_CHANNEL", alignment="hits_align.phy", alg_format="iphylip")
#t.show()
t = Tree(args.trees[0])
#Get leaves
#names = t.get_leaf_names()
#algae = filterNames(names, re.compile('.*ALGA.*').match)
#plants = filterNames(names, re.compile('.*PLANT.*').match)
#colourNodes(t,algae,"green")
#colourNodes(t,plants,"#4ED34E")
circle = TreeStyle()
circle.show_leaf_name = True
#circle.scale = 3
circle.mode = "c"
