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 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):
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 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 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 load_model(node, model):
'''
supra specia action
link to evolutionnary model
'''
model = model['loadmodel']
T = node.get_tree_root()
model = T._models[model]
T.change_dist_to_evol('bL', model, True)
if model.properties['typ'] == 'site':
model.set_histface(up=False,
typ='protamine',
lines=[1.0, 0.3],
col_lines=['black', 'grey'])
I = TreeImageProperties()
I.aligned_foot.add_face(model.properties['histface'], 1)
application.set_img_properties(I)
elif (model.properties['typ'] == 'branch_ancestor'):
I = TreeImageProperties()
for n in sorted(T.get_descendants() + [T], key=lambda x: x.paml_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=11)
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(
faces.TextFace('paml_id: #%d ' % (n.paml_id), fsize=8), 0)
application.set_img_properties(I)
else:
application.set_img_properties(None)
def get_example_tree():
t = Tree()
t.populate(8, reuse_names=False)
ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
return t, ts
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 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 get_example_tree():
t = Tree()
t.populate(10)
# Margins, alignment, border, background and opacity can now be set for any face
rs1 = faces.TextFace("branch-right\nmargins&borders",
fsize=12,
fgcolor="#009000")
rs1.margin_top = 10
rs1.margin_bottom = 50
rs1.margin_left = 40
rs1.margin_right = 40
rs1.border.width = 1
rs1.background.color = "lightgreen"
rs1.inner_border.width = 0
rs1.inner_border.line_style = 1
rs1.inner_border.color = "red"
rs1.opacity = 0.6
rs1.hz_align = 2 # 0 left, 1 center, 2 right
rs1.vt_align = 1 # 0 left, 1 center, 2 right
br1 = faces.TextFace("branch-right1", fsize=12, fgcolor="#009000")
br2 = faces.TextFace("branch-right3", fsize=12, fgcolor="#009000")
# New face positions (branch-top and branch-bottom)
bb = faces.TextFace("branch-bottom 1", fsize=8, fgcolor="#909000")
bb2 = faces.TextFace("branch-bottom 2", fsize=8, fgcolor="#909000")
bt = faces.TextFace("branch-top 1", fsize=6, fgcolor="#099000")
# And faces can also be used as headers or foot notes of aligned
# columns
t1 = faces.TextFace("Header Face", fsize=12, fgcolor="#aa0000")
t2 = faces.TextFace("Footer Face", fsize=12, fgcolor="#0000aa")
# Attribute faces can now contain prefix and suffix fixed text
aligned = faces.AttrFace("name",
fsize=12,
fgcolor="RoyalBlue",
text_prefix="Aligned (",
text_suffix=")")
# horizontal and vertical alignment per face
aligned.hz_align = 1 # 0 left, 1 center, 2 right
aligned.vt_align = 1
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
style = NodeStyle()
style["fgcolor"] = "Gold"
style["shape"] = "square"
style["size"] = 15
style["vt_line_color"] = "#ff0000"
t.set_style(style)
# add a face to the style. This face will be render in any node
# associated to the style.
fixed = faces.TextFace("FIXED branch-right", fsize=11, fgcolor="blue")
t.add_face(fixed, column=1, position="branch-right")
# Bind the precomputed style to the root node
# ETE 2.1 has now support for general image properties
ts = TreeStyle()
# You can add faces to the tree image (without any node
# associated). They will be used as headers and foot notes of the
# aligned columns (aligned faces)
ts.aligned_header.add_face(t1, column=0)
ts.aligned_header.add_face(t1, 1)
ts.aligned_header.add_face(t1, 2)
ts.aligned_header.add_face(t1, 3)
t1.hz_align = 1 # 0 left, 1 center, 2 right
t1.border.width = 1
ts.aligned_foot.add_face(t2, column=0)
ts.aligned_foot.add_face(t2, 1)
ts.aligned_foot.add_face(t2, 2)
ts.aligned_foot.add_face(t2, 3)
t2.hz_align = 1
# Set tree image style. Note that aligned header and foot is only
# visible in "rect" mode.
ts.mode = "r"
ts.scale = 10
for node in t.traverse():
# If node is a leaf, add the nodes name and a its scientific
# name
if node.is_leaf():
node.add_face(aligned, column=0, position="aligned")
node.add_face(aligned, column=1, position="aligned")
node.add_face(aligned, column=3, position="aligned")
else:
node.add_face(bt, column=0, position="branch-top")
node.add_face(bb, column=0, position="branch-bottom")
node.add_face(bb2, column=0, position="branch-bottom")
node.add_face(br1, column=0, position="branch-right")
node.add_face(rs1, column=0, position="branch-right")
node.add_face(br2, column=0, position="branch-right")
return t, ts
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
from ete_dev import TreeStyle
from ete_dev import EvolTree
from ete_dev import faces
tree = EvolTree("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print '\n Running free-ratio model with calculation of ancestral sequences...'
tree.run_model('fb_anc')
#tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id):
if n.is_leaf(): continue
anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(
faces.TextFace('node_id: #%d ' % (n.node_id), fsize=8), 0)
print 'display result of bs_anc model, with ancestral amino acid sequences.'
tree.show(tree_style=I)
print '\nThe End.'
t.populate(size, reuse_names=False)
I = TreeStyle()
I.mode = "r"
I.orientation = 0
I.layout_fn = master_ly
I.margin_left = 100
I.margin_right = 50
I.margin_top = 100
I.arc_start = 45
I.arc_span = 360
I.margin_bottom = 50
I.show_border = True
I.legend_position = 4
I.title.add_face(faces.TextFace("HOLA MUNDO", fsize=30), 0)
I.draw_aligned_faces_as_table = True
def test(node):
if node.is_leaf():
faces.add_face_to_node(faces.AttrFace("name"),
node,
0,
position="aligned")
I.aligned_header.add_face(faces.TextFace("H1"), 0)
I.aligned_header.add_face(faces.TextFace("H1"), 1)
I.aligned_header.add_face(faces.TextFace("H1"), 2)
I.aligned_header.add_face(faces.TextFace("H1111111111111"), 3)
