def test(self):
# Text faces
I = TreeImage()
I.mode = "rect"
I.aligned_header.add_face(self.headerF, 0)
I.aligned_header.add_face(self.headerF, 1)
I.aligned_header.add_face(self.headerF, 2)
I.aligned_header.add_face(self.headerF, 3)
I.aligned_foot.add_face(self.footF, 0)
I.aligned_foot.add_face(self.footF, 1)
I.aligned_foot.add_face(self.footF, 2)
I.aligned_foot.add_face(self.footF, 3)
I.draw_aligned_faces_as_grid = True
t = Tree()
t.dist = 0
t.populate(10)
style = NodeStyleDict()
style["fgcolor"] = "#ff0000"
style["size"] = 20
style.add_fixed_face(self.fixedF, "branch-right", 0)
t.img_style = style
t.render("./test.svg", layout=mylayout, tree_style=I)
t.show(mylayout, tree_style=I)
t.show(mylayout2, tree_style=I)
def get_example_tree():
# Random tree
t = Tree()
t.populate(20, random_branches=True)
# Some random features in all nodes
for n in t.traverse():
n.add_features(weight=random.randint(0, 50))
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
return t, ts
def get_example_tree():
# Random tree
t = Tree()
t.populate(20, random_branches=True)
# Some random features in all nodes
for n in t.traverse():
n.add_features(weight=random.randint(0, 50))
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
return t, ts
def get_example_tree():
# sample sequence and a list of example motif types
seq = "LHGRISQQVEQSRSQVQAIGEKVSLAQAKIEKIKGSKKAIKVFSSAKYPAPERLQEYGSIFTDAQDPGLQRRPRHRIQSKQRPLDERALQEKLKDFPVCVSTKPEPEDDAEEGLGGLPSNISSVSSLLLFNTTENLYKKYVFLDPLAGAVTKTHVMLGAETEEKLFDAPLSISKREQLEQQVPENYFYVPDLGQVPEIDVPSYLPDLPGIANDLMYIADLGPGIAPSAPGTIPELPTFHTEVAEPLKVGELGSGMGAGPGTPAHTPSSLDTPHFVFQTYKMGAPPLPPSTAAPVGQGARQDDSSSSASPSVQGAPREVVDPSGGWATLLESIRQAGGIGKAKLRSMKERKLEKQQQKEQEQVRATSQGGHLMSDLFNKLVMRRKGISGKGPGAGDGPGGAFARVSDSIPPLPPPQQPQAEDEDDWES"
motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
[110, 150, "o", None, 10, "blue", "pink", None],
[155, 180, "()", None, 10, "blue", "rgradient:purple", None],
[160, 170, "^", None, 14, "black", "yellow", None],
[172, 180, "v", None, 12, "black", "rgradient:orange", None],
[185, 190, "o", None, 12, "black", "brown", None],
[198, 200, "<>", None, 15, "black", "rgradient:gold", None],
[210, 240, "compactseq", 2, 10, None, None, None],
[300, 320, "seq", 10, 10, None, None, None],
[310, 345, "<>", None, 15, "black", "rgradient:black", None],
]
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(10)
for l in t.iter_leaves():
seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))
seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
seqtail_format="compactseq", scale_factor=1)
seqFace.margin_bottom = 4
f = l.add_face(seqFace, 0, "aligned")
return t, TreeStyle()
def get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False
t.populate(10)
return t, ts
def get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False
t.populate(10)
return t, ts
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 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 get_example_tree():
t = Tree()
t.populate(10)
ts = TreeStyle()
ts.rotation = 45
ts.show_leaf_name = False
ts.layout_fn = rotation_layout
return t, ts
def get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_leaf_name = True
ts.min_leaf_separation = 15
t.populate(100)
return t, ts
def get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_leaf_name = True
ts.min_leaf_separation = 15
t.populate(100)
return t, ts
def get_example_tree():
t = Tree()
t.populate(8)
# 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)
# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)
#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0
style1["vt_line_color"] = "#ff0000"
style1["hz_line_color"] = "#ff0000"
style1["vt_line_width"] = 2
style1["hz_line_width"] = 2
style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
style1["hz_line_type"] = 2
t.children[0].img_style = style1
t.children[1].img_style = style1
# Set dashed blue lines in all leaves
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
style2["vt_line_color"] = "#0000aa"
style2["hz_line_color"] = "#0000aa"
style2["vt_line_width"] = 2
style2["hz_line_width"] = 2
style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
style2["hz_line_type"] = 1
for l in t.iter_leaves():
l.img_style = style2
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
return t, ts
def get_example_tree():
t = Tree()
t.populate(8)
# 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)
# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)
#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0
style1["vt_line_color"] = "#ff0000"
style1["hz_line_color"] = "#ff0000"
style1["vt_line_width"] = 2
style1["hz_line_width"] = 2
style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
style1["hz_line_type"] = 2
t.children[0].img_style = style1
t.children[1].img_style = style1
# Set dashed blue lines in all leaves
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
style2["vt_line_color"] = "#0000aa"
style2["hz_line_color"] = "#0000aa"
style2["vt_line_width"] = 2
style2["hz_line_width"] = 2
style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
style2["hz_line_type"] = 1
for l in t.iter_leaves():
l.img_style = style2
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
return t, ts
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):
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 get_example_tree():
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(10)
# for l in t.iter_leaves():
# seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))
# seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
# seqtail_format="compactseq", scale_factor=1)
# seqFace.margin_bottom = 4
# f = l.add_face(seqFace, 0, "aligned")
ts = TreeStyle()
ts.layout_fn = layout
t.show(tree_style=ts)
return t, ts
def get_example_tree():
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(10)
# for l in t.iter_leaves():
# seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))
# seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
# seqtail_format="compactseq", scale_factor=1)
# seqFace.margin_bottom = 4
# f = l.add_face(seqFace, 0, "aligned")
ts = TreeStyle()
ts.layout_fn = layout
t.show(tree_style=ts)
return t, ts
def get_example_tree():
# sample sequence and a list of example motif types
seq = "LHGRISQQVEQSRSQVQAIGEKVSLAQAKIEKIKGSKKAIKVFSSAKYPAPERLQEYGSIFTDAQDPGLQRRPRHRIQSKQRPLDERALQEKLKDFPVCVSTKPEPEDDAEEGLGGLPSNISSVSSLLLFNTTENLYKKYVFLDPLAGAVTKTHVMLGAETEEKLFDAPLSISKREQLEQQVPENYFYVPDLGQVPEIDVPSYLPDLPGIANDLMYIADLGPGIAPSAPGTIPELPTFHTEVAEPLKVGELGSGMGAGPGTPAHTPSSLDTPHFVFQTYKMGAPPLPPSTAAPVGQGARQDDSSSSASPSVQGAPREVVDPSGGWATLLESIRQAGGIGKAKLRSMKERKLEKQQQKEQEQVRATSQGGHLMSDLFNKLVMRRKGISGKGPGAGDGPGGAFARVSDSIPPLPPPQQPQAEDEDDWES"
motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[
10, 100, "[]", None, 10, "black", "rgradient:blue",
"arial|8|white|domain Name"
],
[110, 150, "o", None, 10, "blue", "pink", None],
[155, 180, "()", None, 10, "blue", "rgradient:purple", None],
[160, 170, "^", None, 14, "black", "yellow", None],
[172, 180, "v", None, 12, "black", "rgradient:orange", None],
[185, 190, "o", None, 12, "black", "brown", None],
[198, 200, "<>", None, 15, "black", "rgradient:gold", None],
[210, 240, "compactseq", 2, 10, None, None, None],
[300, 320, "seq", 10, 10, None, None, None],
[310, 345, "<>", None, 15, "black", "rgradient:black", None],
]
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(10)
for l in t.iter_leaves():
seq_motifs = [list(m) for m in motifs
] #sample(motifs, randint(2, len(motifs)))
seqFace = SeqMotifFace(seq,
seq_motifs,
intermotif_format="line",
seqtail_format="compactseq",
scale_factor=1)
seqFace.margin_bottom = 4
f = l.add_face(seqFace, 0, "aligned")
return t, TreeStyle()
import time
from ete_dev import Tree
# Creates a random tree with 10,000 leaf nodes
tree = Tree()
tree.populate(10000)
# This code should be faster
t1 = time.time()
for leaf in tree.iter_leaves():
if "aw" in leaf.name:
print "found a match:", leaf.name,
break
print "Iterating: ellapsed time:", time.time() - t1
# This slower
t1 = time.time()
for leaf in tree.get_leaves():
if "aw" in leaf.name:
print "found a match:", leaf.name,
break
print "Getting: ellapsed time:", time.time() - t1
# Results in something like:
# found a match: guoaw Iterating: ellapsed time: 0.00436091423035 secs
# found a match: guoaw Getting: ellapsed time: 0.124316930771 secs
# faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
# node.img_style["bgcolor"] = random_color()
# Tree().show()
ts = TreeStyle()
ts.mode = "c"
ts.layout_fn = layout
ts.show_leaf_name = False
ts.arc_span = 340
ts.arc_start = -70
# ts.allow_face_overlap = True
# ts.show_branch_length = True
ts.draw_guiding_lines = False
ts.optimal_scale_level = "mid"
ts.extra_branch_line_color = "red"
ts.root_opening_factor = 0.50
ts.show_border = True
ts.scale = None
t = Tree()
t.populate(200, random_branches=True, branch_range=(0, 0))
t.dist = 0.0
dists = [n.dist for n in t.traverse() if n.dist != 0]
# print max(dists), min(dists)
t.write(outfile="test.nw")
# for s in [5, None]:
# ts.scale = s
# t.render("img_scale_%s.png" %s, tree_style = ts, w=600)
t.show(tree_style=ts)
from ete_dev import Tree, faces, AttrFace, TreeStyle, NodeStyle
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)
t = Tree()
t.populate(8)
# 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)
# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)
#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0
motifs = [
# seq.start, seq.end, shape, width, height, fgcolor, bgcolor
[120, 130, ">", 34, 13, "black", "red", None],
[145, 150, "<", 60, 5, "black", "green", None],
[10, 30, "o", 100, 10, "black", "rgradient:blue", None],
[20, 50, "[]", 100, 10, "blue", "pink", None],
[55, 80, "()", 100, 10, "blue", "rgradient:purple", None],
[160, 170, "^", 50, 14, "black", "yellow", None],
[172, 180, "v", 20, 12, "black", "rgradient:orange", None],
[185, 190, "o", 12, 12, "black", "brown", None],
[198, 200, "<>", 15, 15, "black", "rgradient:gold", None],
[210, 240, "compactseq", 2, 10, None, None, None],
[300, 320, "seq", 10, 10, None, None, None],
[340, 350, "<>", 15, 15, "black", "rgradient:black", None],
]
# Show usage help for SeqMotifFace
print SeqMotifFace.__doc__
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(40)
for l in t.iter_leaves():
seq_motifs = sample(motifs, randint(2, len(motifs)))
seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line", seqtail_format="compactseq")
seqFace.margin_bottom = 4
f = l.add_face(seqFace, 0, "aligned")
t.show()
# n4.size = (10, 10)
#n2.size = 10
#n3.size = 10
#n5.size = 10
#n2.dist = 0.1
#n2.size = 1
#n3.size = 1
#n2.dist = 0.5
#t.populate(100)#, random_branches=True)
#t.write(outfile="test.nw")
ts.layout_fn = layout2
t.show(tree_style=ts)
ts.scale = 1
sys.exit()
t.show(tree_style=ts)
for x in xrange(30):
t = Tree()
t.dist = 0
t.populate(100, random_branches=True)
t.render("/tmp/kk.png", tree_style=ts)
sys.exit()
ts.layout_fn = layout
t.show(tree_style=ts)
ts.mode = "r"
t.show(tree_style=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")
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False
t.populate(10)
t.show(tree_style=ts)
n = main_tree.add_child()
n.add_face(temp_facet, 0, "aligned")
t, ts = seq_motif_faces.get_example_tree()
temp_facet = TreeFace(t, ts)
n = main_tree.add_child()
n.add_face(temp_facet, 0, "aligned")
t, ts = barchart_and_piechart_faces.get_example_tree()
temp_facet = TreeFace(t, ts)
n = main_tree.add_child()
n.add_face(temp_facet, 0, "aligned")
# Test orphan nodes and trees with 0 branch length
t, ts = Tree(), TreeStyle()
t.populate(5)
for n in t.traverse():
n.dist = 0
temp_tface = TreeFace(t, ts)
n = main_tree.add_child()
n.add_face(temp_tface, 0, "aligned")
ts.optimal_scale_level = "full"
temp_tface = TreeFace(t, ts)
n = main_tree.add_child()
n.add_face(temp_tface, 0, "aligned")
ts = TreeStyle()
t.populate(5)
ts.mode = "c"
temp_tface = TreeFace(t, ts)
#node.img_style["bgcolor"] = random_color()
#Tree().show()
ts = TreeStyle()
ts.mode = "c"
ts.layout_fn = layout
ts.show_leaf_name = False
ts.arc_span = 340
ts.arc_start = -70
#ts.allow_face_overlap = True
#ts.show_branch_length = True
ts.draw_guiding_lines = False
ts.optimal_scale_level = "mid"
ts.extra_branch_line_color = "red"
ts.root_opening_factor = 0.50
ts.show_border = True
ts.scale = None
t = Tree()
t.populate(200, random_branches=True, branch_range=(0, 0))
t.dist = 0.0
dists = [n.dist for n in t.traverse() if n.dist != 0]
#print max(dists), min(dists)
t.write(outfile="test.nw")
#for s in [5, None]:
# ts.scale = s
# t.render("img_scale_%s.png" %s, tree_style = ts, w=600)
t.show(tree_style=ts)
# n.size = (10, 10)
# n2.size = (10, 70)
# n3.size = (40, 40)
# n4.size = (10, 10)
#n2.size = 10
#n3.size = 10
#n5.size = 10
#n2.dist = 0.1
#n2.size = 1
#n3.size = 1
#n2.dist = 0.5
#t.populate(100)#, random_branches=True)
#t.write(outfile="test.nw")
ts.layout_fn = layout2
t.show(tree_style=ts)
ts.scale = 1
sys.exit()
t.show(tree_style=ts)
for x in xrange(30):
t = Tree()
t.dist = 0
t.populate(100, random_branches=True)
t.render("/tmp/kk.png", tree_style=ts)
sys.exit()
ts.layout_fn = layout
t.show(tree_style=ts)
ts.mode = "r"
t.show(tree_style=ts)
from ete_dev import Tree
t = Tree()
# Generate a random tree with 50 leaves
t.populate(50)
# Render tree in png and pdf format using the default size
t.render("./random_tree.png")
t.render("./random_tree.pdf")
# Render tree in pdf setting a custom width. height will be imputed
t.render("./random_tree.pdf", w=300)
# Render tree in pdf setting a custom height. Width will be imputed
t.render("./random_tree.pdf", h=600)
# Render tree in pdf setting a custom width and height
t.render("./random_tree.pdf", w=300, h=300)
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
# Center text according to masterItem size
tw = text.boundingRect().width()
th = text.boundingRect().height()
center = masterItem.boundingRect().center()
text.setPos(center.x()-tw/2, center.y()-th/2)
return masterItem
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")
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)
t.render("item_faces.png", h=400, tree_style=ts)
# The interactive features are only available using the GUI
t.show(tree_style=ts)
def master_ly(node):
random_background(node)
sphere_map(node)
leaf_name(node)
aligned_faces(node)
def tiny_ly(node):
node.img_style["size"] = 2
node.img_style["shape"] = "square"
size = 15
t = Tree()
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)
import sys
from ete_dev import Tree, faces, TreeStyle, COLOR_SCHEMES
sys.path.insert(0, "./")
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")
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False
t.populate(10)
t.show(tree_style=ts)
from ete_dev import Tree
t = Tree()
# Generate a random tree with 50 leaves
t.populate(50)
# Render tree in png and pdf format using the default size
t.render("./random_tree.png")
t.render("./random_tree.pdf")
# Render tree in pdf setting a custom width. height will be imputed
t.render("./random_tree.pdf", w=300)
# Render tree in pdf setting a custom height. Width will be imputed
t.render("./random_tree.pdf", h=600)
# Render tree in pdf setting a custom width and height
t.render("./random_tree.pdf", w=300, h=300)
from ete_dev import Tree # generates a random tree t = Tree() t.populate(15) print t # # # /-qogjl # /--------| # | \-vxbgp # | # | /-xyewk #---------| | # | | /-opben # | | | # | | /--------| /-xoryn # \--------| | | /--------| # | | | | | /-wdima # | | \--------| \--------| # | | | \-qxovz # | | | # | | \-isngq # \--------| # | /-neqsc # | | # | | /-waxkv # | /--------| /--------| # | | | /--------| \-djeoh # | | | | | # | | \--------| \-exmsn # \--------| |
],
[160, 170, "^", 50, 14, "black", "yellow", None],
[172, 180, "v", 20, 12, "black", "rgradient:orange", None],
[185, 190, "o", 12, 12, "black", "brown", "Arial|12|white|Domain"],
[198, 200, "<>", 15, 15, "black", "rgradient:gold", None],
[210, 240, "compactseq", 2, 10, None, None, None],
[300, 320, "seq", 20, 20, None, None, "Courier|10|red|TestName"],
[
340, 350, "<>", 15, 15, "black", "rgradient:black",
"Arial|12|black|HOLASEQ"
],
]
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(20)
for l in t.iter_leaves():
# For each leaf, we create a random list of motifs from the original list.
seq_motifs = sample(motifs, randint(2, len(motifs)))
# And we add it as a Sequence Motif Face.
seqFace = SeqMotifFace(seq,
seq_motifs,
intermotif_format="line",
seqtail_format="compactseq")
seqFace.margin_bottom = 4
f = l.add_face(seqFace, 0, "aligned")
t.render("seq_motif_faces.png", w=1000)
#t.show()
from ete_dev import Tree # generates a random tree t = Tree(); t.populate(15); print t # # # /-qogjl # /--------| # | \-vxbgp # | # | /-xyewk #---------| | # | | /-opben # | | | # | | /--------| /-xoryn # \--------| | | /--------| # | | | | | /-wdima # | | \--------| \--------| # | | | \-qxovz # | | | # | | \-isngq # \--------| # | /-neqsc # | | # | | /-waxkv # | /--------| /--------| # | | | /--------| \-djeoh # | | | | | # | | \--------| \-exmsn # \--------| |
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
import time
from ete_dev import Tree
# Creates a random tree with 10,000 leaf nodes
tree = Tree()
tree.populate(10000)
# This code should be faster
t1 = time.time()
for leaf in tree.iter_leaves():
if "aw" in leaf.name:
print "found a match:", leaf.name,
break
print "Iterating: ellapsed time:", time.time()-t1
# This slower
t1 = time.time()
for leaf in tree.get_leaves():
if "aw" in leaf.name:
print "found a match:", leaf.name,
break
print "Getting: ellapsed time:", time.time()-t1
# Results in something like:
# found a match: guoaw Iterating: ellapsed time: 0.00436091423035 secs
# found a match: guoaw Getting: ellapsed time: 0.124316930771 secs
faces.add_face_to_node(F, node, i, position="aligned")
def master_ly(node):
random_background(node)
sphere_map(node)
leaf_name(node)
aligned_faces(node)
def tiny_ly(node):
node.img_style["size"] = 2
node.img_style["shape"] = "square"
size = 15
t = Tree()
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)