def sel_mylayout(node):
node.set_style(my_node_style)
if node.is_leaf():
# add names in larger font + italics
species_name = AttrFace("name", fsize=12, fstyle="italic")
add_face_to_node(species_name,
node,
column=0,
position="branch-right")
# add absence/presence matrix
for i, value in enumerate(getattr(node, "profile", [])):
if value > 0:
color = "#FF0000"
else:
color = "#EEEEEE"
my_face = CircleFace(8, color, style="circle")
my_face.margin_right = 3
my_face.margin_bottom = 3
add_face_to_node(my_face, node, position="aligned", column=i)
def build_colorful_tree(newick, filename=""):
"""
Note that these will fail if we dont have all the pre-reqs and it is not triival to get them all.
This stuff is NOT general purpose.
"""
from ete3 import Tree, TreeStyle, CircleFace, TextFace
tree = Tree(newick)
#setup colors and treestyle
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.force_topology = True
ts.arc_span = 360
face = CircleFace(30, "MediumSeaGreen")
face.margin_top = 1000
ts.legend.add_face(face, column=0)
face = TextFace("Normal B-cell", fsize=64)
face.margin_right = 100
face.margin_top = 1000
ts.legend.add_face(face, column=1)
ts.legend.add_face(CircleFace(30, "SeaGreen"), column=0)
face = TextFace("Normal B CD19pcell", fsize=64)
face.margin_right = 100
ts.legend.add_face(face, column=1)
ts.legend.add_face(CircleFace(30, "ForestGreen"), column=0)
face = TextFace("Normal B CD19pCD27pcell", fsize=64)
face.margin_right = 100
ts.legend.add_face(face, column=1)
ts.legend.add_face(CircleFace(30, "Green"), column=0)
face = TextFace("Normal B CD19pCD27mcell", fsize=64)
face.margin_right = 100
ts.legend.add_face(face, column=1)
ts.legend.add_face(CircleFace(30, "RoyalBlue"), column=0)
face = TextFace("CLL all-batches", fsize=64)
face.margin_right = 100
ts.legend.add_face(face, column=1)
#draw tree
from ete3 import NodeStyle
styles = {}
styles["normal_B"] = NodeStyle(bgcolor="MediumSeaGreen",
hz_line_color="Black",
vt_line_color="Black")
styles["NormalBCD19pcell"] = NodeStyle(bgcolor="SeaGreen",
hz_line_color="Black",
vt_line_color="Black")
styles["NormalBCD19pCD27pcell"] = NodeStyle(bgcolor="ForestGreen",
hz_line_color="Black",
vt_line_color="Black")
styles["NormalBCD19pCD27mcell"] = NodeStyle(bgcolor="Green",
hz_line_color="Black",
vt_line_color="Black")
styles["CLL"] = NodeStyle(bgcolor="RoyalBlue",
hz_line_color="Black",
vt_line_color="Black")
for node in tree.traverse("postorder"):
#print node.set_style()
if len(node.get_leaf_names()) == 1:
name = node.get_leaf_names()[0]
if "normal_B" in name:
node.set_style(styles["normal_B"])
elif "NormalBCD19pcell" in name:
node.set_style(styles["NormalBCD19pcell"])
elif "NormalBCD19pCD27pcell" in name:
node.set_style(styles["NormalBCD19pCD27pcell"])
elif "NormalBCD19pCD27mcell" in name:
node.set_style(styles["NormalBCD19pCD27mcell"])
else:
node.set_style(styles["CLL"])
#lol
tree.render(filename, w=10, dpi=600, units='in', tree_style=ts)