def phylogeny(node):
leaf_color = "#000000"
node.img_style["shape"] = "circle"
if hasattr(node, "evoltype"):
if node.evoltype == 'D':
node.img_style["fgcolor"] = "#FF0000"
node.img_style["hz_line_color"] = "#FF0000"
node.img_style["vt_line_color"] = "#FF0000"
elif node.evoltype == 'S':
node.img_style["fgcolor"] = "#1d176e"
node.img_style["hz_line_color"] = "#1d176e"
node.img_style["vt_line_color"] = "#1d176e"
elif node.evoltype == 'L':
node.img_style["fgcolor"] = "#777777"
node.img_style["vt_line_color"] = "#777777"
node.img_style["hz_line_color"] = "#777777"
node.img_style["hz_line_type"] = 1
node.img_style["vt_line_type"] = 1
leaf_color = "#777777"
if node.is_leaf():
node.img_style["shape"] = "square"
node.img_style["size"] = 4
node.img_style["fgcolor"] = leaf_color
faces.add_face_to_node(
faces.AttrFace("name", "Arial", 11, leaf_color, None), node, 0)
if hasattr(node, "sequence"):
SequenceFace = faces.SequenceFace(node.sequence, "aa", 13)
faces.add_face_to_node(SequenceFace, node, 1, aligned=True)
else:
node.img_style["size"] = 6
def evol_clean_layout(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
leaf_color = "#000000"
node.img_style["size"] = 2
if node.is_leaf():
#if hasattr (node,"highlight"):
# faces.add_face_to_node(faces.AttrFace("name", "Arial", 9, \
# node.highlight,
# None), \
# node, 0 )
#else:
# leaface = faces.AttrFace("name", "Arial", 9, leaf_color, None)
# leaface.margin_right = 10
# faces.add_face_to_node (leaface, node, 0)
if hasattr (node, "sequence"):
seqface = faces.SequenceFace(node.sequence, interactive=True,
codon=node.nt_sequence)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if hasattr (node, 'dN'):
faces.add_face_to_node (faces.TextFace('%.4f'%(node.w), fsize=6,
fgcolor="#7D2D2D"),
node, 0, position="branch-top")
faces.add_face_to_node (faces.TextFace('%.2f/%.2f'% (100*node.dN,
100*node.dS),
fsize=6, fgcolor="#787878"),
node, 0, position="branch-bottom")
if hasattr(node,"extras"):
faces.add_face_to_node( faces.AttrFace("extras", "Arial", 7, \
"#000000", None), node, 2 )
def evol_layout(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"] = False
leaf_color = "#000000"
if not node.is_root() and 'w' in node.features:
node.img_style["shape"] = 'circle'
if (node.w > 900):
node._w = 3
elif (node.w > 100):
node._w = 2.5
elif (node.w > 10):
node._w = 2
elif (node.w > 1):
node._w = 1.5
else:
node._w = node.w
node.img_style["size"] = int((float(node._w)) * 6 + 2)
if node._w == 3:
node.img_style["fgcolor"] = "#c10000"
if node._w == 2.5:
node.img_style["fgcolor"] = "#FF5A02"
if node._w == 2:
node.img_style["fgcolor"] = "#FFA200"
if node._w == 1.5:
node.img_style["fgcolor"] = "#E9BF00"
if node._w < 0.2:
node.img_style["fgcolor"] = "#000000"
if hasattr(node, "extras"):
faces.add_face_to_node( faces.AttrFace("extras", "Arial", 7, \
"#000000", None), node, 2 )
#if node.is_leaf():
if hasattr(node, "sequence"):
seqface = faces.SequenceFace(node.sequence,
interactive=True,
codon=node.nt_sequence)
faces.add_face_to_node(seqface, node, 1, aligned=True)