def master_layout(node):
node.img_style["shape"] = "square"
node.img_style["fgcolor"] = "steelblue"
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"] = node.bgcolor
N = faces.AttrFace("name", fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N, node, 0, position="branch-top")
if node.is_leaf():
node.img_style["size"] = 0
for aname, pos in LEAF_ATTRIBUTES.iteritems():
if aname == "sequence":
N = faces.SeqMotifFace(node.sequence, seq_format="compactseq")
faces.add_face_to_node(N, node, pos, position="aligned")
else:
N = faces.AttrFace(aname, fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N,
node,
pos,
position=LEAF_NAME_POSITION)
else:
node.img_style["size"] = 5
for aname, pos in INTERNAL_ATTRIBUTES.iteritems():
N = faces.AttrFace(aname, fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N, node, pos, position=LEAF_NAME_POSITION)
def master_layout(node):
node.img_style["shape"] = "square"
node.img_style["fgcolor"] = "steelblue"
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"] = node.bgcolor
N = faces.AttrFace("name", fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N, node, 0, position="branch-top")
if node.is_leaf():
node.img_style["size"] = 0
for aname, pos in LEAF_ATTRIBUTES.iteritems():
if aname == "sequence":
N = faces.SeqMotifFace(node.sequence, seq_format="compactseq")
faces.add_face_to_node(N, node, pos, position="aligned")
else:
N = faces.AttrFace(aname, fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N, node, pos, position=LEAF_NAME_POSITION)
else:
node.img_style["size"] = 5
for aname, pos in INTERNAL_ATTRIBUTES.iteritems():
N = faces.AttrFace(aname, fsize=NAME_FONT_SIZE)
N.margin_left = 1
faces.add_face_to_node(N, node, pos, position=LEAF_NAME_POSITION)
def ncbi_layout(node):
npr_layout(node)
global name2color
if node.is_leaf():
tax_pos = 10
if hasattr(node, "lineage"):
for tax,k in zip(node.lineage, node.named_lineage):
f = faces.TextFace("%10s" %k, fsize=15)
try:
color = name2color[k]
except KeyError:
name2color[k] = color = treeview.main.random_color()
#if hasattr(node, "broken_groups") and tax in node.broken_groups:
f.background.color = color
faces.add_face_to_node(f, node, tax_pos, position="aligned")
tax_pos += 1
f = faces.AttrFace("spname", fsize=15)
faces.add_face_to_node(f, node, 10, position="branch-right")
else:
if getattr(node, "broken_groups", None):
for broken in node.broken_groups:
f = faces.TextFace(broken, fsize=10, fgcolor="red")
faces.add_face_to_node(f, node, 1, position="branch-bottom")
if getattr(node, "broken_levels", None):
for broken in node.broken_levels:
f = faces.TextFace(broken, fsize=10, fgcolor="blue")
faces.add_face_to_node(f, node, 1, position="branch-bottom")
if hasattr(node, "changed"):
if node.changed == "yes":
node.img_style["bgcolor"]="indianred"
else:
node.img_style["bgcolor"]="white"
def ncbi_layout(node):
npr_layout(node)
global name2color
if node.is_leaf():
tax_pos = 10
if hasattr(node, "lineage"):
for tax, k in zip(node.lineage, node.named_lineage):
f = faces.TextFace("%10s" % k, fsize=15)
try:
color = name2color[k]
except KeyError:
name2color[k] = color = treeview.main.random_color()
#if hasattr(node, "broken_groups") and tax in node.broken_groups:
f.background.color = color
faces.add_face_to_node(f, node, tax_pos, position="aligned")
tax_pos += 1
f = faces.AttrFace("spname", fsize=15)
faces.add_face_to_node(f, node, 10, position="branch-right")
else:
if getattr(node, "broken_groups", None):
for broken in node.broken_groups:
f = faces.TextFace(broken, fsize=10, fgcolor="red")
faces.add_face_to_node(f, node, 1, position="branch-bottom")
if getattr(node, "broken_levels", None):
for broken in node.broken_levels:
f = faces.TextFace(broken, fsize=10, fgcolor="blue")
faces.add_face_to_node(f, node, 1, position="branch-bottom")
if hasattr(node, "changed"):
if node.changed == "yes":
node.img_style["bgcolor"] = "indianred"
else:
node.img_style["bgcolor"] = "white"
def npr_layout(node):
if node.is_leaf():
name = faces.AttrFace("name", fsize=12)
faces.add_face_to_node(name, node, 0, position="branch-right")
if hasattr(node, "sequence"):
seq_face = faces.SeqFace(node.sequence, [])
faces.add_face_to_node(seq_face, node, 0, position="aligned")
if "alg_type" in node.features:
faces.add_face_to_node(faces.AttrFace("alg_type", fsize=8),
node,
0,
position="branch-top")
ttype = faces.AttrFace("tree_type", fsize=8, fgcolor="DarkBlue")
faces.add_face_to_node(ttype, node, 0, position="branch-top")
#ttype.background.color = "DarkOliveGreen"
node.img_style["size"] = 20
node.img_style["fgcolor"] = "red"
if "treemerger_rf" in node.features:
faces.add_face_to_node(faces.AttrFace("treemerger_rf", fsize=8),
node,
0,
position="branch-bottom")
support_radius = (1.0 - node.support) * 50
if not node.is_leaf() and support_radius > 1:
support_face = faces.CircleFace(support_radius, "red")
faces.add_face_to_node(support_face, node, 0, position="float-behind")
support_face.opacity = 0.25
faces.add_face_to_node(faces.AttrFace("support", fsize=8),
node,
0,
position="branch-bottom")
if "clean_alg_mean_identn" in node.features:
identity = node.clean_alg_mean_identn
elif "alg_mean_identn" in node.features:
identity = node.alg_mean_identn
if "highlighted" in node.features:
node.img_style["bgcolor"] = "LightCyan"
if "npr_iter" in node.features:
node.img_style["size"] = 50
if "improve" in node.features:
color = "orange" if float(node.improve) < 0 else "green"
if float(node.improve) == 0:
color = "blue"
support_face = faces.CircleFace(200, color)
faces.add_face_to_node(support_face, node, 0, position="float-behind")
def npr_layout(node):
if node.is_leaf():
name = faces.AttrFace("name", fsize=12)
faces.add_face_to_node(name, node, 0, position="branch-right")
if hasattr(node, "sequence"):
seq_face = faces.SeqFace(node.sequence, [])
faces.add_face_to_node(seq_face, node, 0, position="aligned")
if "alg_type" in node.features:
faces.add_face_to_node(faces.AttrFace("alg_type", fsize=8), node, 0, position="branch-top")
ttype=faces.AttrFace("tree_type", fsize=8, fgcolor="DarkBlue")
faces.add_face_to_node(ttype, node, 0, position="branch-top")
#ttype.background.color = "DarkOliveGreen"
node.img_style["size"] = 20
node.img_style["fgcolor"] = "red"
if "treemerger_rf" in node.features:
faces.add_face_to_node(faces.AttrFace("treemerger_rf", fsize=8), node, 0, position="branch-bottom")
support_radius= (1.0 - node.support) * 50
if not node.is_leaf() and support_radius > 1:
support_face = faces.CircleFace(support_radius, "red")
faces.add_face_to_node(support_face, node, 0, position="float-behind")
support_face.opacity = 0.25
faces.add_face_to_node(faces.AttrFace("support", fsize=8), node, 0, position="branch-bottom")
if "clean_alg_mean_identn" in node.features:
identity = node.clean_alg_mean_identn
elif "alg_mean_identn" in node.features:
identity = node.alg_mean_identn
if "highlighted" in node.features:
node.img_style["bgcolor"] = "LightCyan"
if "npr_iter" in node.features:
node.img_style["size"] = 50
if "improve" in node.features:
color = "orange" if float(node.improve) < 0 else "green"
if float(node.improve) == 0:
color = "blue"
support_face = faces.CircleFace(200, color)
faces.add_face_to_node(support_face, node, 0, position="float-behind")
