def create_circle(self,
filename,
title,
name2color=None,
name2class_dic=None,
class2color_dic=None,
vector=None,
ignore_branch_length=True):
plt.clf()
axis_font = {'size': '3'}
plt.rc('xtick', labelsize=0.1)
plt.rc('ytick', labelsize=0.1)
plt.rc({'font.size': 0.1})
# legend creation
if name2class_dic and class2color_dic:
leg = []
for cls, color in class2color_dic.items():
leg.append(mpatches.Patch(color=color, label=cls))
t = Tree(self.nwk)
# iterate over tree leaves only
for l in t.iter_leaves():
ns = NodeStyle()
if name2color:
ns["bgcolor"] = name2color[
l.name] if l.name in name2color else 'white'
elif name2class_dic and class2color_dic:
ns["bgcolor"] = class2color_dic[name2class_dic[
l.name]] if l.name in name2class_dic else 'white'
# Gray dashed branch lines
#ns["hz_line_type"] = 1
#ns["hz_line_color"] = "#cccccc"
#
l.img_style = ns
F = TextFace(l.name)
F.ftype = 'Times'
#if vector:
# if l.name in vector:
l.add_features(profile=[random.random()
for x in range(10)]) #vector[l.name])
l.add_features(deviation=[0 for x in range(10)
]) #len(vector[l.name]))])
l.add_face(ProfileFace(max_v=1,
min_v=0.0,
center_v=0.5,
width=200,
height=40,
style='heatmap',
colorscheme=5),
column=0,
position='aligned')
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = VisualizeCircularTree.layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
ts.force_topology = ignore_branch_length
ts.title.add_face(TextFace(title, fsize=20, ftype='Times'), column=15)
# legend creation
if name2class_dic and class2color_dic:
for k, (cls, col) in enumerate(class2color_dic.items()):
x = RectFace(8, 8, 'black', col)
#x.opacity=0.5
ts.legend.add_face(x, column=8)
ts.legend.add_face(TextFace(' ' + cls + ' ',
fsize=9,
ftype='Times'),
column=9)
t.render(filename + '.pdf', tree_style=ts, dpi=5000)
