def master_ly(node):
if node.is_leaf():
# Create an ItemFAce. First argument must be the pointer to
# the constructor function that returns a QGraphicsItem. It
# will be used to draw the Face. Next arguments are arbitrary,
# and they will be forwarded to the constructor Face function.
F = faces.DynamicItemFace(ugly_name_face, 100, 50)
faces.add_face_to_node(F, node, 0, position="aligned")
def master_ly(node):
if node.is_leaf():
# Create an ItemFAce. First argument must be the pointer to
# the constructor function that returns a QGraphicsItem. It
# will be used to draw the Face. Next arguments are arbitrary,
# and they will be forwarded to the constructor Face function.
F = faces.DynamicItemFace(ugly_name_face, 100, 50)
faces.add_face_to_node(F, node, 0, position="aligned")
def layout(node):
if not node.is_leaf():
size = random.randint(20,50)
F= faces.PieChartFace([10,20,60,10],
colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]],
width=size, height=size)
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F,node, 0, position="float")
def layout(node):
if not node.is_leaf():
size = random.randint(20, 50)
F = faces.PieChartFace([10, 20, 60, 10],
colors=COLOR_SCHEMES[random.sample(
schema_names, 1)[0]],
width=size,
height=size)
F.border.width = None
F.opacity = 0.6
faces.add_face_to_node(F, node, 0, position="float")
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
global CONT
if CONT >= len(chars):
CONT = 0
if node.is_leaf():
node.img_style["size"] = 0
F2= AttrFace("name", tight_text=True)
F= TextFace(chars[CONT], tight_text=True)
F.inner_border.width = 0
F2.inner_border.width = 0
#faces.add_face_to_node(F ,node, 0, position="branch-right")
faces.add_face_to_node(F2 ,node, 1, position="branch-right")
CONT += 1
def test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
if "weight" in node.features:
# Creates a sphere face whose size is proportional to node's
# feature "weight"
C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
# Let's make the sphere transparent
C.opacity = 0.3
# And place as a float face over the tree
faces.add_face_to_node(C, node, 0, position="float")
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
t = Tree()
t.populate(10)
T = TreeFace(t, small_ts)
# Let's make the sphere transparent
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
faces.add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
faces.add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
# If silhouette is good, creates a green bubble
if node.silhouette > 0:
validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"] = "#056600"
# Otherwise, use red bubbles
else:
validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
"Verdana", 10, "#940000")
node.img_style["fgcolor"] = "#940000"
# Sets node size proportional to the silhouette value.
node.img_style["shape"] = "sphere"
if node.silhouette <= 1 and node.silhouette >= -1:
node.img_style["size"] = 15 + int((abs(node.silhouette) * 10)**2)
# If node is very internal, draw also a bar diagram
# with the average expression of the partition
faces.add_face_to_node(validationFace, node, 0)
if len(node) > 100:
faces.add_face_to_node(cbarsFace, node, 1)
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
faces.add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=0
faces.add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
# If silhouette is good, creates a green bubble
if node.silhouette>0:
validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#056600")
node.img_style["fgcolor"]="#056600"
# Otherwise, use red bubbles
else:
validationFace = faces.TextFace("Silh=%0.2f" %node.silhouette, "Verdana", 10, "#940000")
node.img_style["fgcolor"]="#940000"
# Sets node size proportional to the silhouette value.
node.img_style["shape"]="sphere"
if node.silhouette<=1 and node.silhouette>=-1:
node.img_style["size"]= 15+int((abs(node.silhouette)*10)**2)
# If node is very internal, draw also a bar diagram
# with the average expression of the partition
faces.add_face_to_node(validationFace, node, 0)
if len(node)>100:
faces.add_face_to_node(cbarsFace, node, 1)
def layout(node):
if node.is_leaf():
# Add node name to laef nodes
N = AttrFace("name", fsize=14, fgcolor="black")
faces.add_face_to_node(N, node, 0)
t = Tree()
t.populate(10)
T = TreeFace(t, small_ts)
# Let's make the sphere transparent
T.opacity = 0.8
# And place as a float face over the tree
faces.add_face_to_node(T, node, 1, position="aligned")
def layout(node):
node.img_style["size"] = random.randint(5, 100)
node.img_style["hz_line_width"] = 5
node.img_style["vt_line_width"] = 10
if node.is_leaf():
# node.img_style["size"] = random.randint(50, 50)
f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
# f = faces.AttrFace("name", fsize=random.randint(20,20))
faces.add_face_to_node(f, node, 0, position="aligned")
f.border.width = 0
# f = faces.CircleFace(20, "red")
# f = faces.AttrFace("name", fsize=20)
f = faces.TextFace("NAME", fsize=10)
# faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
def layout2(node):
#node.img_style["size"] = random.randint(40, 200)
if hasattr(node, "size"):
f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
faces.add_face_to_node(f, node, 0, position="branch-top")
faces.add_face_to_node(f, node, 0, position="branch-bottom")
#f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
node.img_style["size"] = 10
node.img_style["shape"] = "square"
node.img_style["bgcolor"] = random_color()
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
def test_layout_phylo_nt(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"] = False
if node.is_leaf():
if hasattr(node, "sequence"):
seqface = MySequenceFace(node.sequence,
"nt",
fsize=10,
col_w=11,
interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def layout(node):
node.img_style["size"] = random.randint(5,100)
node.img_style["hz_line_width"] = 5
node.img_style["vt_line_width"] = 10
if node.is_leaf():
#node.img_style["size"] = random.randint(50, 50)
f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
#f = faces.AttrFace("name", fsize=random.randint(20,20))
faces.add_face_to_node(f, node, 0, position="aligned")
f.border.width = 0
#f = faces.CircleFace(20, "red")
#f = faces.AttrFace("name", fsize=20)
f = faces.TextFace("NAME", fsize=10)
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
def layout2(node):
#node.img_style["size"] = random.randint(40, 200)
if hasattr(node, "size"):
f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
faces.add_face_to_node(f, node, 0, position="branch-top")
faces.add_face_to_node(f, node, 0, position="branch-bottom")
#f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
node.img_style["size"] = 10
node.img_style["shape"] = "square"
node.img_style["bgcolor"] = random_color()
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
def test_layout_phylo_aa_motif(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "aa",
fsize=10,special_col=special_col,
alt_col_w=3,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def test_layout_phylo_aa_motif(node):
'''
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"] = False
special_col = [[10, 100], [150, 1000], [1000, 2000], [3000, 4990]]
if node.is_leaf():
if hasattr(node, "sequence"):
seqface = MySequenceFace(node.sequence,
"aa",
fsize=10,
special_col=special_col,
alt_col_w=3,
col_w=11,
interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
def aligned_faces(node):
if node.is_leaf():
for i in xrange(3):
F = faces.TextFace("ABCDEFGHIJK"[0:random.randint(1, 11)])
F.border.width = 1
F.border.line_style = 1
F.inner_background.color = "lightgreen"
F.border.width = 1
F.inner_border.width = 1
F.background.color = "darkgreen"
F.border.width = 2
F.vt_align = random.randint(0, 4)
F.hz_align = random.randint(0, 4)
F.margin_bottom = random.randint(1, 20)
F.margin_right = random.randint(1, 20)
F.margin_left = random.randint(1, 20)
F.margin_top = random.randint(1, 20)
faces.add_face_to_node(F, node, i, position="aligned")
if random.randint(0, 1):
faces.add_face_to_node(F, node, i, position="aligned")
def aligned_faces(node):
if node.is_leaf():
for i in xrange(3):
F = faces.TextFace("ABCDEFGHIJK"[0:random.randint(1,11)])
F.border.width = 1
F.border.line_style = 1
F.inner_background.color = "lightgreen"
F.border.width = 1
F.inner_border.width = 1
F.background.color = "darkgreen"
F.border.width = 2
F.vt_align = random.randint(0,4)
F.hz_align = random.randint(0,4)
F.margin_bottom = random.randint(1, 20)
F.margin_right = random.randint(1, 20)
F.margin_left = random.randint(1, 20)
F.margin_top = random.randint(1, 20)
faces.add_face_to_node(F, node, i, position="aligned")
if random.randint(0, 1):
faces.add_face_to_node(F, node, i, position="aligned")
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 hasattr(node, "changed"):
if node.changed == "yes":
node.img_style["bgcolor"] = "indianred"
else:
node.img_style["bgcolor"] = "white"
def layout(node):
if node.is_leaf():
F = faces.PieChartFace([10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6],
colors=COLOR_SCHEMES["set3"],
width=50,
height=50)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
F = faces.PieChartFace([10, 20, 5, 5, 60],
colors=COLOR_SCHEMES[random.sample(
schema_names, 1)[0]],
width=100,
height=40)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
else:
F = faces.BarChartFace(
[40, 20, 70, 100, 30, 40, 50, 40, 70, 12],
min_value=0,
colors=COLOR_SCHEMES["spectral"],
labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","))
faces.add_face_to_node(F, node, 0, position="branch-top")
F.background.color = "#eee"
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 hasattr(node, "changed"):
if node.changed == "yes":
node.img_style["bgcolor"]="indianred"
else:
node.img_style["bgcolor"]="white"
def layout(node):
if node.is_leaf():
F= faces.PieChartFace([10,10,10,10,10,10,10,10,10,4,6], colors=COLOR_SCHEMES["set3"], width=100, height=100)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F,node, 0, position="branch-right")
F.background.color = "indianred"
x = faces.TextFace("hola")
faces.add_face_to_node(x,node, 1, position="branch-right")
x.background.color = "blue"
else:
F= faces.BarChartFace([40,20,70,100,30,40,50,40,70,12], min_value=0, colors=COLOR_SCHEMES["spectral"])
faces.add_face_to_node(F,node, 0, position="branch-top")
def layout(node):
if node.is_leaf():
F = faces.PieChartFace([10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6],
colors=COLOR_SCHEMES["set3"],
width=100,
height=100)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
F.background.color = "indianred"
x = faces.TextFace("hola")
faces.add_face_to_node(x, node, 1, position="branch-right")
x.background.color = "blue"
else:
F = faces.BarChartFace([40, 20, 70, 100, 30, 40, 50, 40, 70, 12],
min_value=0,
colors=COLOR_SCHEMES["spectral"])
faces.add_face_to_node(F, node, 0, position="branch-top")
def layout(node):
if node.is_leaf():
F = faces.PieChartFace(
[10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6], colors=COLOR_SCHEMES["set3"], width=50, height=50
)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
F = faces.PieChartFace(
[10, 20, 5, 5, 60], colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]], width=100, height=40
)
F.border.width = None
F.opacity = 0.8
faces.add_face_to_node(F, node, 0, position="branch-right")
else:
F = faces.BarChartFace(
[40, 20, 70, 100, 30, 40, 50, 40, 70, 12],
min_value=0,
colors=COLOR_SCHEMES["spectral"],
labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","),
)
faces.add_face_to_node(F, node, 0, position="branch-top")
F.background.color = "#eee"
def layout(node):
node.img_style["size"] = 5
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
if node.is_leaf():
f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
faces.add_face_to_node(f, node, 0, position="aligned")
f = faces.AttrFace("name", fsize=15)
faces.add_face_to_node(f, node, 0, position="branch-right")
else:
f = faces.TextFace("uno", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-top")
f = faces.TextFace("otromassssssssssss", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-bottom")
f = faces.CircleFace(20, "red")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float")
f = faces.CircleFace(23, "blue")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float-behind")
def test(node):
if node.is_leaf():
faces.add_face_to_node(faces.AttrFace("name"), node, 0, position="aligned")
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# Add an static face that handles the node name
faces.add_face_to_node(nameFace, node, column=0)
# We can also create faces on the fly
longNameFace = faces.TextFace(code2name[node.name])
faces.add_face_to_node(longNameFace, node, column=0)
# text faces support multiline. We add a text face
# with the whole description of each leaf.
descFace = faces.TextFace(code2desc[node.name], fsize=10)
# Note that this faces is added in "aligned" mode
faces.add_face_to_node(descFace, node, column=0, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "circle"
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 6
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "#000000"
# If an internal node contains more than 4 leaves, add the
# images of the represented species sorted in columns of 2
# images max.
if len(node) >= 4:
col = 0
for i, name in enumerate(set(node.get_leaf_names())):
if i > 0 and i % 2 == 0:
col += 1
# Add the corresponding face to the node
if name.startswith("Dme"):
faces.add_face_to_node(flyFace, node, column=col)
elif name.startswith("Dre"):
faces.add_face_to_node(fishFace, node, column=col)
elif name.startswith("Mms"):
faces.add_face_to_node(mouseFace, node, column=col)
elif name.startswith("Ptr"):
faces.add_face_to_node(chimpFace, node, column=col)
elif name.startswith("Hsa"):
faces.add_face_to_node(humanFace, node, column=col)
elif name.startswith("Cfa"):
faces.add_face_to_node(dogFace, node, column=col)
# Modifies this node's style
node.img_style["size"] = 16
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#AA0000"
# If leaf is "Hsa" (h**o sapiens), highlight it using a
# different background.
if node.is_leaf() and node.name.startswith("Hsa"):
node.img_style["bgcolor"] = "#9db0cf"
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 "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 sphere_map(node):
# Creates a random color sphere face that will be floating over nodes
bubble = faces.CircleFace(random.randint(5, 40), random_color(), "sphere")
bubble.opacity = 0.7
faces.add_face_to_node(bubble, node, 0, position="float")
def leaf_name(node):
if node.is_leaf():
nameF = faces.AttrFace("name")
nameF.border.width = 1
faces.add_face_to_node(nameF, node, 0, position="branch-right")
def mylayout(node):
T = TestTreeview
node.img_style["size"]=random.sample(range(4,30),1)[0]
if node.is_leaf():
faces.add_face_to_node(T.nameF, node, column=0, position="aligned")
faces.add_face_to_node(T.nameF, node, column=2, position="aligned")
faces.add_face_to_node(T.nameF, node, column=3, position="aligned")
else:
faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
faces.add_face_to_node(T.downF, node, column=1, position="branch-bottom")
faces.add_face_to_node(T.downF, node, column=1, position="branch-bottom")
faces.add_face_to_node(T.rF1, node, column=1, position="branch-right")
faces.add_face_to_node(T.rF2, node, column=1, position="branch-right")
faces.add_face_to_node(T.rF3, node, column=2, position="branch-right")
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 "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 layout(node):
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0)
def main_layout(node):
''' Main layout function. It controls what is shown in tree
images. '''
# Add faces to leaf nodes. This allows me to add the faces from
# the global variable LEAVE_FACES, which is set by the application
# controler according to the arguments passed through the URL.
if node.is_leaf():
for f, fkey, pos in LEAVE_FACES:
if hasattr(node, fkey):
faces.add_face_to_node(f, node, column=pos, position="branch-right")
else:
# Add special faces on collapsed nodes
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"]= False
collapsed_face = faces.TextFace(\
" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
# Set node aspect. This controls which node features are used to
# control the style of the tree. You can add or modify this
# features, as well as their behaviour
if node.is_leaf():
node.img_style["shape"] = "square"
node.img_style["size"] = 4
else:
node.img_style["size"] = 8
node.img_style["shape"] = "sphere"
# Evoltype: [D]uplications, [S]peciations or [L]osess.
if hasattr(node,"evoltype"):
if node.evoltype == 'D':
node.img_style["fgcolor"] = "#1d176e"
node.img_style["hz_line_color"] = "#1d176e"
node.img_style["vt_line_color"] = "#1d176e"
elif node.evoltype == 'S':
node.img_style["fgcolor"] = "#FF0000"
node.img_style["line_color"] = "#FF0000"
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["line_type"] = 1
# If no evolutionary information, set a default style
else:
node.img_style["fgcolor"] = "#000000"
node.img_style["vt_line_color"] = "#000000"
node.img_style["hz_line_color"] = "#000000"
# Parse node features features and conver them into styles. This
# must be done like this, since current ete version does not allow
# modifying style outside the layout function.
if hasattr(node, "bsize"):
node.img_style["size"]= int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"]= node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"]= node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"]= node.fgcolor
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
faces.add_face_to_node(aligned, node, column=0, position="aligned")
faces.add_face_to_node(aligned, node, column=1, position="aligned")
faces.add_face_to_node(aligned, node, column=3, position="aligned")
else:
faces.add_face_to_node(bt, node, column=0, position="branch-top")
faces.add_face_to_node(bb, node, column=0, position="branch-bottom")
faces.add_face_to_node(bb2, node, column=0, position="branch-bottom")
faces.add_face_to_node(br1, node, column=0, position="branch-right")
faces.add_face_to_node(rs1, node, column=0, position="branch-right")
faces.add_face_to_node(br2, node, column=0, position="branch-right")
def layout(node):
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
faces.add_face_to_node(AttrFace("name"), node, column=0)
def layout(node):
node.img_style["size"] = 5
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
if node.is_leaf():
f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
faces.add_face_to_node(f, node, 0, position="aligned")
f = faces.AttrFace("name", fsize=15)
faces.add_face_to_node(f, node, 0, position="branch-right")
else:
f = faces.TextFace("uno", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-top")
f = faces.TextFace("otromassssssssssss", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-bottom")
f = faces.CircleFace(20, "red")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float")
f = faces.CircleFace(23, "blue")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float-behind")
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=30)
faces.add_face_to_node(N, node, 0, position="aligned")
def leaf_name(node):
if node.is_leaf():
nameF = faces.AttrFace("name")
nameF.border.width = 1
faces.add_face_to_node(nameF, node, 0, position="branch-right")
def main_layout(node):
''' Main layout function. It controls what is shown in tree
images. '''
# Add faces to leaf nodes. This allows me to add the faces from
# the global variable LEAVE_FACES, which is set by the application
# controler according to the arguments passed through the URL.
if node.is_leaf():
for f, fkey, pos in LEAVE_FACES:
if hasattr(node, fkey):
faces.add_face_to_node(f,
node,
column=pos,
position="branch-right")
else:
# Add special faces on collapsed nodes
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"] = False
collapsed_face = faces.TextFace(\
" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
# Set node aspect. This controls which node features are used to
# control the style of the tree. You can add or modify this
# features, as well as their behaviour
if node.is_leaf():
node.img_style["shape"] = "square"
node.img_style["size"] = 4
else:
node.img_style["size"] = 8
node.img_style["shape"] = "sphere"
# Evoltype: [D]uplications, [S]peciations or [L]osess.
if hasattr(node, "evoltype"):
if node.evoltype == 'D':
node.img_style["fgcolor"] = "#1d176e"
node.img_style["hz_line_color"] = "#1d176e"
node.img_style["vt_line_color"] = "#1d176e"
elif node.evoltype == 'S':
node.img_style["fgcolor"] = "#FF0000"
node.img_style["line_color"] = "#FF0000"
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["line_type"] = 1
# If no evolutionary information, set a default style
else:
node.img_style["fgcolor"] = "#000000"
node.img_style["vt_line_color"] = "#000000"
node.img_style["hz_line_color"] = "#000000"
# Parse node features features and conver them into styles. This
# must be done like this, since current ete version does not allow
# modifying style outside the layout function.
if hasattr(node, "bsize"):
node.img_style["size"] = int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"] = node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"] = node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"] = node.fgcolor
def codeml_clean_layout(node):
'''
layout for CodemlTree
'''
for f, fkey, pos in LEAVE_FACES:
if hasattr(node, fkey):
if not (fkey == 'name' and node.name == 'NoName'):
if node.is_leaf():
faces.add_face_to_node(f,
node,
column=pos,
position="branch-right")
elif fkey == 'species':
if node.species != "Unknown":
faces.add_face_to_node(faces.TextFace(
' (%s)' % (node.species),
fsize=6,
fgcolor="#787878"),
node,
-1,
position="branch-bottom")
else:
faces.add_face_to_node(f,
node,
column=pos,
position="branch-bottom")
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 not node.is_leaf():
node.img_style["shape"] = "sphere"
node.img_style["size"] = 5
# Add special faces on collapsed nodes
if hasattr(node, "hide") and int(node.hide) == 1:
node.img_style["draw_descendants"] = False
collapsed_face = faces.TextFace(\
" %s collapsed leaves." %len(node), \
fsize=10, fgcolor="#444", ftype="Arial")
faces.add_face_to_node(collapsed_face, node, 0)
else:
node.img_style["draw_descendants"] = True
else:
node.img_style["size"] = 2
node.img_style["shape"] = "square"
if hasattr(node, "sequence"):
seqface = faces.SequenceFace(node.sequence, "aa", 11)
faces.add_face_to_node(seqface, node, 1, aligned=True)
leaf_color = "#000000"
node.img_style["fgcolor"] = leaf_color
if hasattr(node, "bsize"):
node.img_style["size"] = int(node.bsize)
if hasattr(node, "shape"):
node.img_style["shape"] = node.shape
if hasattr(node, "bgcolor"):
node.img_style["bgcolor"] = node.bgcolor
if hasattr(node, "fgcolor"):
node.img_style["fgcolor"] = node.fgcolor
def layout(node):
if node.is_leaf():
N = AttrFace("name", fsize=30)
faces.add_face_to_node(N, node, 0, position="aligned")
def test(node):
if node.is_leaf():
faces.add_face_to_node(faces.AttrFace("name"),
node,
0,
position="aligned")
def mylayout(node):
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
# Add an static face that handles the node name
faces.add_face_to_node(nameFace, node, column=0)
# We can also create faces on the fly
longNameFace = faces.TextFace(code2name[node.name])
faces.add_face_to_node(longNameFace, node, column=0)
# text faces support multiline. We add a text face
# with the whole description of each leaf.
descFace = faces.TextFace(code2desc[node.name], fsize=10)
descFace.margin_top = 10
descFace.margin_bottom = 10
descFace.border.margin = 1
# Note that this faces is added in "aligned" mode
faces.add_face_to_node(descFace, node, column=0, aligned=True)
# Sets the style of leaf nodes
node.img_style["size"] = 12
node.img_style["shape"] = "circle"
#If node is an internal node
else:
# Sets the style of internal nodes
node.img_style["size"] = 6
node.img_style["shape"] = "circle"
node.img_style["fgcolor"] = "#000000"
# If an internal node contains more than 4 leaves, add the
# images of the represented species sorted in columns of 2
# images max.
if len(node)>=4:
col = 0
for i, name in enumerate(set(node.get_leaf_names())):
if i>0 and i%2 == 0:
col += 1
# Add the corresponding face to the node
if name.startswith("Dme"):
faces.add_face_to_node(flyFace, node, column=col)
elif name.startswith("Dre"):
faces.add_face_to_node(fishFace, node, column=col)
elif name.startswith("Mms"):
faces.add_face_to_node(mouseFace, node, column=col)
elif name.startswith("Ptr"):
faces.add_face_to_node(chimpFace, node, column=col)
elif name.startswith("Hsa"):
faces.add_face_to_node(humanFace, node, column=col)
elif name.startswith("Cfa"):
faces.add_face_to_node(dogFace, node, column=col)
# Modifies this node's style
node.img_style["size"] = 16
node.img_style["shape"] = "sphere"
node.img_style["fgcolor"] = "#AA0000"
# If leaf is "Hsa" (h**o sapiens), highlight it using a
# different background.
if node.is_leaf() and node.name.startswith("Hsa"):
node.img_style["bgcolor"] = "#9db0cf"
def sphere_map(node):
# Creates a random color sphere face that will be floating over nodes
bubble = faces.CircleFace(random.randint(5,40), random_color(), "sphere")
bubble.opacity = 0.7
faces.add_face_to_node(bubble, node, 0, position="float")