def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=0
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 = TextFace("Silh=%0.2f" %node.silhouette,
"Verdana", 10, "#056600")
node.img_style["fgcolor"]="#056600"
# Otherwise, use red bubbles
else:
validationFace = 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
add_face_to_node(validationFace, node, 0)
if len(node)>100:
add_face_to_node(cbarsFace, node, 1)
def __init__(self, tree, alg_type=None, ncbitaxa=True):
self.tree = tree
self.tree.dist = 0
self.svg = None
self.layouts = None
self.treestyle = TreeStyle()
self.alg_type = alg_type
ts = self.treestyle
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.tree_width = 250
ts.layout_fn = [self.ly_basic, self.ly_leaf_names, self.ly_supports]
self.ncbitaxa = ncbitaxa
if ncbitaxa:
ts.layout_fn.append(self.ly_tax_labels)
if self.alg_type == 'condensed':
ts.layout_fn.append(self.ly_condensed_alg)
elif self.alg_type == 'block':
ts.layout_fn.append(self.ly_block_alg)
self.TRACKED_CLADES = set()
if ncbitaxa:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
for lf in tree:
for lname in getattr(lf, 'named_lineage', [])[2:9]:
self.TRACKED_CLADES.add(lname.lower())
self.TRACKED_CLADES.update(map(lower, ["Eukaryota", "Viridiplantae", "Fungi", "birds", "Basidiomycota", "Ascomycota",
"Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta", "mammalia", "Primates",
"Amoebozoa", "Crypthophyta", "Bacteria","Archaea", "Arthropoda", "rodentia", "laurastheria",
"Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
"Gammaproteobacteria",]))
colors = random_color(num=len(self.TRACKED_CLADES), s=0.45)
self.LIN2COLOR = dict([(ln, colors[i]) for i, ln in enumerate(sorted(self.TRACKED_CLADES))])
self.LIN2FACE = {}
for tname in self.TRACKED_CLADES:
linF = TextFace(tname, fsize=10, fgcolor='white', tight_text=False, ftype="Arial")
linF.margin_left = 3
linF.margin_right = 2
linF.inner_background.color = self.LIN2COLOR[tname.lower()]
self.LIN2FACE[tname.lower()] = linF
self.LABEL_START_COL = 100
self.ALG_START_COL = len(self.TRACKED_CLADES)+11
#tree.ladderize()
self.svg, self.img_map = tree.render("%%return", tree_style=ts)
def rotation_layout(node):
if node.is_leaf():
F = TextFace(node.name, tight_text=True)
F.rotation = randint(0, 360)
add_face_to_node(TextFace("third" ), node, column=8, position="branch-right")
add_face_to_node(TextFace("second" ), node, column=2, position="branch-right")
add_face_to_node(F, node, column=0, position="branch-right")
F.border.width = 1
F.inner_border.width = 1
def ly_leaf_names(self, node):
if node.is_leaf():
if node.species != 0 and self.ncbitaxa:
spF = TextFace("%s" %getattr(node, "spname", ""), fsize=8, fgcolor='#777777', ftype='Helvetica')
geneF = TextFace("(%s)" %node.name[:50], fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
add_face_to_node(geneF, node, column=1, position='branch-right')
else:
geneF = TextFace("%s" %node.name, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=0, position='branch-right')
def ly_tax_labels(node):
if node.is_leaf():
c = LABEL_START_COL
largest = 0
for tname in TRACKED_CLADES:
if hasattr(node, "named_lineage") and tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.margin_right = 2
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_tax_labels(self, node):
if node.is_leaf():
c = self.LABEL_START_COL
node_lin = getattr(node, "named_lineage", [])
for tname in node_lin:
if tname.lower() in self.TRACKED_CLADES:
linF = self.LIN2FACE[tname.lower()]
# linF = TextFace(tname, fsize=10, fgcolor='white')
# linF.margin_left = 3
# linF.margin_right = 2
# linF.background.color = self.LIN2COLOR[tname.lower()]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(c, len(self.TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def get_example_tree():
t = Tree("((a,b),c);")
right_c0_r0 = TextFace("right_col0_row0")
right_c0_r1 = TextFace("right_col0_row1")
right_c1_r0 = TextFace("right_col1_row0")
right_c1_r1 = TextFace("right_col1_row1")
right_c1_r2 = TextFace("right_col1_row2")
top_c0_r0 = TextFace("top_col0_row0")
top_c0_r1 = TextFace("top_col0_row1")
bottom_c0_r0 = TextFace("bottom_col0_row0")
bottom_c1_r0 = TextFace("bottom_col1_row0")
aligned_c0_r0 = TextFace("aligned_col0_row0")
aligned_c0_r1 = TextFace("aligned_col0_row1")
aligned_c1_r0 = TextFace("aligned_col1_row0")
aligned_c1_r1 = TextFace("aligned_col1_row1")
t.add_face(right_c0_r1, column=1, position="branch-right")
t.add_face(right_c0_r0, column=0, position="branch-right")
t.add_face(right_c1_r2, column=2, position="branch-right")
t.add_face(right_c1_r1, column=1, position="branch-right")
t.add_face(right_c1_r0, column=0, position="branch-right")
t.add_face(top_c0_r1, column=1, position="branch-top")
t.add_face(top_c0_r0, column=0, position="branch-top")
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c1_r0, column=1, position="branch-bottom")
for leaf in t.iter_leaves():
leaf.add_face(aligned_c0_r1, 0, "aligned")
leaf.add_face(aligned_c0_r0, 0, "aligned")
leaf.add_face(aligned_c1_r1, 0, "aligned")
leaf.add_face(aligned_c1_r0, 0, "aligned")
return t, TreeStyle()
TTG GGA CTG GTC GGC TTC AAG GCA GTA AGT CAA TTC GTA ATA CGT CGT GCG
>Chimp
CAC GCC CGA TGG CTC AAC GAA AAG TTA AGA TGC GAA TTG AGA ACT CTG AAA AAA
TTG GGA CTG GAC GGC TAC AAG GCA GTA AGT CAG TAC GTT AAA GGT CGT GCG
>Orangutan
GAT GCA CGC TGG ATC AAC GAA AAG TTA AGA TGC GTA TCG AGA ACT CTG AAA AAA
TTG GGA CTG GAC GGC TAC AAG GGA GTA AGT CAA TAC GTT AAA GGT CGT CCG
""")
#try:
# tree.run_model("fb")
# tree.run_model("M2")
#except:
# pass
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace(
"Example for EvolTree, interactivity shows codons", fsize=15),
column=0)
ts.layout_fn = test_layout_evol
#try:
# tree.show(tree_style=ts, histfaces=["M2"])
#except:
tree.show(tree_style=ts)
except:
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment("""
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
def ly_supports(self, node):
if not node.is_leaf():
supFace = TextFace("%0.3g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(
' (%s)' % node.name.split()[0].replace("/exon2", ""),
fsize=10,
fgcolor='slategrey',
tight_text=False),
node,
1,
position='branch-right')
add_face_to_node(TextFace(node.species,
fsize=12,
fgcolor='black',
fstyle='italic',
tight_text=False),
node,
0,
position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20 - (c - 1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
node,
c,
position='aligned')
c += 1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c + 1 == len(node.sequence):
start, end = last_lt, c
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c - 1
w = end - start
motifs.append([
start, end, "[]", w, 13, "slategrey",
"slategrey", None
])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence,
motifs,
intermotif_format="line",
seqtail_format="line",
scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' % node.support,
fsize=11,
fgcolor='indianred'),
node,
0,
position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' % float(node.support2),
fsize=11,
fgcolor='steelblue'),
node,
0,
position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
def ly(node):
node.img_style['vt_line_width'] = 1
node.img_style['hz_line_width'] = 1
if node.is_leaf():
add_face_to_node(TextFace(' (%s)' %node.name.split()[0].replace("/exon2", ""), fsize=10, fgcolor='slategrey', tight_text=False), node, 1, position='branch-right')
add_face_to_node(TextFace(node.species, fsize=12, fgcolor='black', fstyle='italic', tight_text=False), node, 0, position='branch-right')
c = 1
for tname in tracked_clades:
if tname in node.named_lineage:
linF = TextFace(tname, fsize=10, fgcolor='white')
linF.margin_left = 3
linF.background.color = lin2color[tname]
add_face_to_node(linF, node, c, position='aligned')
c += 1
for n in xrange(1, 20-(c-1)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
if draw_alg and 'sequence' in node.features:
#seqFace = SequenceFace(node.sequence,"aa",13)
seqFace = SeqMotifFace(node.sequence, [])
# [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
motifs = []
last_lt = None
for c, lt in enumerate(node.sequence):
if lt != '-':
if last_lt is None:
last_lt = c
if c+1 == len(node.sequence):
start, end = last_lt, c
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
w = end-start
motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
last_lt = None
if not motifs:
print node, node.sequence
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=1)
add_face_to_node(seqFace, node, 20, aligned=True)
else:
if node.up:
add_face_to_node(TextFace('% 3g' %node.support, fsize=11, fgcolor='indianred'), node, 0, position='branch-top')
if hasattr(node, "support2") and node.up:
add_face_to_node(TextFace('% 3g' %float(node.support2), fsize=11, fgcolor='steelblue'), node, 0, position='branch-bottom')
node.img_style['size'] = 0
node.img_style['hz_line_color'] = 'black'
node.img_style['vt_line_color'] = 'black'
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
""")
nt_sequences = {
"Human":
"GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
"Chimp":
"CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
"Orangutan":
"GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG"
}
for l in nt_sequences:
(tree & l).nt_sequence = nt_sequences[l]
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("Example for nucleotides...", fsize=15),
column=0)
ts.layout_fn = test_layout_evol
tree.show(tree_style=ts)
# Show very large algs
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]))
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace(
"better not set interactivity if alg is very large", fsize=15),
column=0)
ts.layout_fn = test_layout_phylo_aa
