def layout(node):
#print(node)
if (len(node.get_ancestors()) < 4):
print(node.name)
n = AttrFace("name", fsize=9)
n.margin_top = 10
n.margin_bottom = 0
n.margin_left = 10
faces.add_face_to_node(n, node, 0, position="float")
tf = TextFace(len(node.get_leaves()), fsize=12)
faces.add_face_to_node(tf, node, 0, position="float")
def ete_layout(node):
"""
Formatting of tree nodes while tree is rendered
:param node: ete node
"""
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 0
nstyle["vt_line_width"] = 1 # line width of vertical branches
nstyle["hz_line_width"] = 1 # line width of horizontal branches
node.set_style(nstyle)
if 'median_vaf' in node.features and not np.isnan(
node.median_vaf) and logger.isEnabledFor(logging.DEBUG):
# # Creates a sphere face whose size is proportional to the given VAF or CCF of the acquired muts
# cf = CircleFace(radius=node.median_vaf*50, color="RoyalBlue", style="sphere")
# # Let's make the sphere transparent
# cf.opacity = 0.6
# # And place as a float face over the tree
# faces.add_face_to_node(cf, node, column=0, position="float-behind")
vaf_face = TextFace('({:.0%}) '.format(node.median_vaf),
fsize=9,
fgcolor='SlateGray')
vaf_face.opacity = 0.8 # from 0 to 1
faces.add_face_to_node(vaf_face, node, column=2, position="branch-top")
if node.is_root():
# tf_root = TextFace(node.name, fsize=14, fgcolor="Black")
# tf_root.margin_bottom = 25
# faces.add_face_to_node(tf_root, node, column=0, position='branch-right')
return
bt_face_muts = AttrFace("dist",
fsize=11,
fgcolor="Black",
text_prefix=' ',
text_suffix=' ',
formatter='%d')
bt_face_muts.margin_bottom = 2
bt_face_muts.margin_top = 2
faces.add_face_to_node(bt_face_muts, node, column=1, position="branch-top")
if 'drivers' in node.features and len(node.drivers) > 0:
drivers_face = TextFace(node.drivers,
fsize=11,
fstyle='italic',
fgcolor='OrangeRed')
drivers_face.opacity = 0.8 # from 0 to 1
drivers_face.margin_left = 1
drivers_face.margin_right = 1
faces.add_face_to_node(drivers_face,
node,
column=0,
position="branch-top")
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
# for colors see: http://etetoolkit.org/docs/latest/reference/reference_treeview.html#color-names
leaf_face = AttrFace("name",
fsize=14,
fgcolor="Black",
text_prefix=' ',
text_suffix=' ')
if node.name.startswith('PT') or node.name.startswith(
'Primary'): # primary tumor sample
leaf_face.fgcolor = 'SteelBlue'
elif node.name.startswith('LiM'): # liver met
leaf_face.fgcolor = 'DarkOliveGreen'
elif node.name.startswith('LuM'): # lung met
leaf_face.fgcolor = 'SaddleBrown'
elif node.name.startswith('NoM'): # lymph node met
leaf_face.fgcolor = 'DarkViolet'
elif node.name.startswith('PeM'): # peritoneal met
leaf_face.fgcolor = 'Purple'
elif node.name.startswith('Met') or node.name.startswith(
'M'): # some metastasis
leaf_face.fgcolor = 'Magenta'
elif node.name.startswith('BrM'): # brain met
leaf_face.fgcolor = 'Crimson'
leaf_face.border.type = 0
leaf_face.border.width = 1
leaf_face.margin_bottom = 1
leaf_face.margin_top = 1
faces.add_face_to_node(leaf_face, node,
column=1) # , position="aligned"
else: # inner node
# if not np.isnan(node.support):
# bt_face_conf = AttrFace("support", fsize=12, fgcolor="DimGrey", text_prefix=' ',
# text_suffix=' ', formatter='%0.2f')
if node.confidence is not None and node.confidence != '':
tf_conf = TextFace(node.confidence, fsize=12, fgcolor='DimGrey')
tf_conf.margin_left = 3
tf_conf.margin_right = 3
faces.add_face_to_node(tf_conf,
node,
column=1,
position="branch-bottom")