def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
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
motifs.append([
start, end, "()", 0, 12, "slategrey",
"slategrey", None
])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c - 1
motifs.append([
start, end, "()", 0, 12, "grey", "slategrey",
None
])
last_lt = None
seqFace = SeqMotifFace(node.sequence,
motifs,
intermotif_format="line",
seqtail_format="line",
scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
def my_layout(node):
name = getattr(node, attribute_name)
try:
kmer_full = locale.format("%d", int(node.kmers_full), grouping=True),
except AttributeError:
kmer_full = None
try:
kmer_reduced = locale.format("%d", int(node.kmers_reduced), grouping=True)
except AttributeError:
kmer_reduced = None
if kmer_full is None:
if kmer_reduced is None:
t = name
else:
t = "{} [red. {}]".format(name, kmer_reduced)
else:
if kmer_reduced is None:
t = "{} [full {}]".format(name, kmer_full)
else:
t = "{} [full {} & red. {}]".format(name, kmer_full, kmer_reduced)
f = ete3.TextFace(t, tight_text=True)
ete3.add_face_to_node(f, node, column=0, position="branch-right")
def my_layout(node): #coloca o nome em cada nó
node.name
F = TextFace(
node.name.replace("*", "\n"),
tight_text=True) #substitui onde tem estrela p quebra de linha
add_face_to_node(F, node, column=0, position="branch-right")
F.rotation = -90 #rotação do nome no nó
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)
def my_layout(node):
if node.is_leaf() and any(
[node.name == x.split(';')[-1] for x in selection['Taxonomy_UniEuk']]):
F = ete3.TextFace(node.name, tight_text=True, fgcolor='red')
else:
F = ete3.TextFace(node.name, tight_text=True)
ete3.add_face_to_node(F, node, column=0, position="branch-right")
def ly_block_alg(node):
if node.is_leaf():
if 'sequence' in node.features:
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
motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
last_lt = None
elif lt == '-':
if last_lt is not None:
start, end = last_lt, c-1
motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
last_lt = None
seqFace = SeqMotifFace(node.sequence, motifs,
intermotif_format="line",
seqtail_format="line", scale_factor=ALG_SCALE)
add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica')
add_face_to_node(geneF, node, column=1, position='branch-right')
def custom_layout(node):
if node.is_leaf():
aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=14)
add_face_to_node(aligned_name_face, node, column=2, position='aligned')
name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
add_face_to_node(name_face, node, column=2, position='branch-right')
node.img_style['size'] = 0
if node.name in tip2info:
# For some reason img urls are very slow!
#img_face = ImgFace(tip2info[node.name][0], is_url=True)
#add_face_to_node(img_face, node, column=4, position='branch-right')
habitat_face = TextFace(tip2info[node.name][2], fsize=11, fgcolor='white')
habitat_face.background.color = 'steelblue'
habitat_face.margin_left = 3
habitat_face.margin_top = 3
habitat_face.margin_right = 3
habitat_face.margin_bottom = 3
add_face_to_node(habitat_face, node, column=3, position='aligned')
else:
node.img_style['size'] = 4
node.img_style['shape'] = 'square'
if node.name:
name_face = TextFace(node.name, fgcolor='grey', fsize=10)
name_face.margin_bottom = 2
add_face_to_node(name_face, node, column=0, position='branch-top')
if node.support:
support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
add_face_to_node(support_face, node, column=0, position='branch-bottom')
def tree_profile_layout(node):
if node.is_leaf(
): # the aligned leaf is "column 0", thus traits go to column+1
node.set_style(
ns1) ## may be postponed to when we have ancestral states
ete3.add_face_to_node(ete3.AttrFace("name",
fsize=label_font_size,
text_suffix=" "),
node,
0,
position="aligned")
for column, (rgb_val, lab) in enumerate(
zip(d_seq[node.name], d_seq_lab[
node.name])): ## colour of csv.loc[node.name, "adm2"]
label = {
"text": lab[:10],
"color": "Black",
"fontsize": label_font_size - 1
}
ete3.add_face_to_node(ete3.RectFace(50,
10,
fgcolor=rgb_val,
bgcolor=rgb_val,
label=label),
node,
column + 1,
position="aligned")
else:
node.set_style(ns2)
def my_layout(node):
F = TextFace("\t" + node.name,
tight_text=True,
fstyle="bold",
fsize=40,
fgcolor="black")
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-bottom")
def my_layout(node):
F = TextFace(node.name, tight_text=True)
F.fsize=6
F.margin_left=5
F.margin_right=5
F.margin_top=0
F.margin_bottom=15
F.rotation=-90
add_face_to_node(F, node, column=0, position="branch-right")
def branch_category_layout(node):
nstyle = ete3.NodeStyle()
nstyle['size'] = 0
nstyle["hz_line_width"] = nstyle["vt_line_width"] = 1
nstyle["hz_line_color"] = node.color
nstyle["vt_line_color"] = node.color
nlabel = node.name+'|'+str(node.numerical_label)
nlabelFace = ete3.TextFace(nlabel, fsize=4, fgcolor=node.color)
ete3.add_face_to_node(face=nlabelFace, node=node, column=1, aligned=False, position="branch-right")
node.set_style(nstyle)
def my_layout(node):
# print(dir(node))
# if node.nodetype == 'leaf':
# node_face = TextFace(node.name, tight_text=True)
# node_face.background.color = "LightGreen"
#
# elif node.nodetype == 'node':
if not node.is_leaf():
node_face = TextFace(node.name, tight_text=True)
add_face_to_node(node_face, node, column=0)
def _node_layout(node):
global _circle_tested
node.img_style["size"] = 0
if node.is_leaf():
if node.name not in annotation:
print('Got unknown leaf "%s"' % (node.name))
return
size = annotation[node.name]
else:
children = COMMA.join(sorted([leaf.name for leaf in node]))
if children not in annotation:
print('Got unknown node ' + children)
return
size = annotation[children]
dimension = 4 * math.sqrt(size)
labeld = {
'text': "%d" % (size),
'color': 'white',
'font': 'Helvetica',
'size': 8
}
if size % 2:
clabel = dict(labeld)
if size == 35:
if not _circle_tested:
_circle_tested = True
clabel['text'] = 'Ly'
clabel['size'] = 12
thisFace = ete.CircleFace(dimension / 2,
"steelblue",
"circle",
label=clabel)
elif size == 43:
clabel['size'] = 6
del clabel['color']
thisFace = ete.CircleFace(dimension / 2,
"steelblue",
"sphere",
label=clabel)
else:
thisFace = ete.CircleFace(dimension / 2,
"steelblue",
"sphere",
label="%d" % (size))
else:
thisFace = ete.RectFace(dimension,
dimension,
'green',
'blue',
label=labeld)
thisFace.opacity = 0.7
ete.add_face_to_node(thisFace, node, column=0, position="float")
textF = ete.TextFace(str(size), fsize=12, fgcolor="steelblue")
ete.add_face_to_node(textF, node, column=0, position="aligned")
def branch_state_layout(node):
nstyle = ete3.NodeStyle()
nstyle['size'] = 0
nstyle["hz_line_width"] = nstyle["vt_line_width"] = 1
nstyle["hz_line_color"] = node.color
nstyle["vt_line_color"] = node.color
if node.is_leaf():
nlabel = str(node.state)+'|'+node.name
else:
nlabel = str(node.state)
nlabelFace = ete3.TextFace(nlabel, fsize=6, fgcolor=node.color)
ete3.add_face_to_node(face=nlabelFace, node=node, column=1, aligned=False, position="branch-right")
node.set_style(nstyle)
def my_layout(node):
F = TextFace(node.name, tight_text=True, penwidth=5, fsize=12)
if node.name is not 'a':
add_face_to_node(F, node, column=0, position="branch-right")
node.set_style(ns)
if node.name in families:
G = TextFace(families[node.name], fstyle='italic')
add_face_to_node(G, node, column=0, position="branch-right")
node.set_style(ns)
if node.name in dict_genera:
H = TextFace(dict_genera[node.name], fstyle='italic')
add_face_to_node(H, node, column=0, position="branch-right")
node.set_style(ns)
if node.name in dict_species:
I = TextFace(dict_species[node.name], fstyle='italic')
add_face_to_node(I, node, column=0, position="branch-right")
node.set_style(ns)
if node.name == 'sumatrana':
dict_species[node.name] = '(Sumatran Torrent Frog)'
# if node.is_leaf():
# node.img_style["size"] = 0
# img = ImgFace('/home/stine/Desktop/{}.jpg'.format(node.name))
# add_face_to_node(img, node, column=0, aligned=True)
for n in Anura.iter_search_nodes():
if n.dist > 1:
n.img_style = ns
def add_img(node):
nodeimg = getattr(node, 'img', None)
if nodeimg:
if nodeimg.startswith('//'):
nodeimg = 'https:' + nodeimg
#await ?
ete3.add_face_to_node(ete3.ImgFace(
nodeimg,
width=int(node.imgwidth),
height=int(node.imgheight),
is_url=True),
node,
column=1,
position='branch-right')
def mylayout(node):
node.set_style(ns)
if not node.is_leaf():
ete3.add_face_to_node(ete3.TextFace(node.name),
node,
column=0,
position='branch-top')
ete3.add_face_to_node(ete3.TextFace('\n'.join(
getattr(node, 'info', []))),
node,
column=0,
position='branch-bottom')
if node.support <= 0.5:
node.set_style(dashed_branch)
add_img(node)
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 range(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
c+=1
def ly_leaf_names(node):
if node.is_leaf():
spF = TextFace(node.species,
fsize=10,
fgcolor='#444444',
fstyle='italic',
ftype='Helvetica')
add_face_to_node(spF, node, column=0, position='branch-right')
if hasattr(node, 'genename'):
geneF = TextFace(" (%s)" % node.genename,
fsize=8,
fgcolor='#777777',
ftype='Helvetica')
add_face_to_node(geneF,
node,
column=1,
position='branch-right')
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
def myLayout(node):
if node.is_leaf():
node.img_style['size'] = 0
genome_name, gene_name = node.name.split('_')
node.name = genome_table.loc[genome_name, 'organism_name']
ete3.add_face_to_node(nameFaces[genome_table.loc[genome_name,
'phylum']],
node,
2,
aligned=True)
elif node.is_root():
node.img_style['size'] = 0
else:
if node.support >= 90:
node.img_style['size'] = 5
node.img_style['fgcolor'] = '#a20417'
else:
node.img_style['size'] = 0
def layout(node):
node.img_style["size"] = 0
#add boostrap in not-leaf nodes
if not node.is_leaf():
boostFace = faces.TextFace(node.support, fgcolor="grey", fsize=34)
add_face_to_node(boostFace, node, column=0, position="branch-top")
if node.is_leaf():
#get taxid and name
taxid = (node.name.split('.')[0])
seq_name = (node.name.split('.')[1])
#add predicted name (eggnog-mapper)
try:
pred_name = predict_name[node.name]
predNameFace = faces.TextFace(pred_name,
fgcolor="salmon",
fsize=34)
predNameFace.margin_right = 20
predNameFace.margin_left = 20
add_face_to_node(predNameFace,
node,
column=2,
position="branch-right")
except:
predNameFace = faces.TextFace('--', fgcolor="salmon", fsize=34)
add_face_to_node(predNameFace,
node,
column=2,
position="branch-right")
#add sequence name (seq_name)
seqNameFace = faces.TextFace(seq_name, fgcolor="grey", fsize=34)
add_face_to_node(seqNameFace, node, column=1, position="branch-right")
#get scientific name from taxid
sp_name = ncbi.get_taxid_translator([(node.name.split('.')[0])])
node.name = sp_name[int(taxid)]
#add alignment
seqFace = SeqMotifFace(node.sequence, gap_format="blank")
add_face_to_node(seqFace, node, column=3, position="aligned")
def _node_layout(node):
global _circle_tested
node.img_style["size"] = 0
if node.is_leaf():
if node.name not in annotation:
print('Got unknown leaf "%s"' % (node.name))
return
size = annotation[node.name]
else:
children = COMMA.join(sorted([leaf.name for leaf in node]))
if children not in annotation:
print('Got unknown node ' + children)
return
size = annotation[children]
dimension = 4*math.sqrt(size)
labeld = {
'text' : "%d" % (size),
'color' : 'white',
'font' : 'Helvetica',
'size' : 8
}
if size % 2:
clabel = dict(labeld)
if size == 35:
if not _circle_tested:
_circle_tested = True
clabel['text'] = 'Ly'
clabel['size'] = 12
thisFace = ete.CircleFace(dimension/2, "steelblue", "circle", label=clabel)
elif size == 43:
clabel['size'] = 6
del clabel['color']
thisFace = ete.CircleFace(dimension/2, "steelblue", "sphere", label=clabel)
else:
thisFace = ete.CircleFace(dimension/2, "steelblue", "sphere", label="%d" % (size))
else:
thisFace = ete.RectFace(dimension, dimension, 'green', 'blue', label=labeld)
thisFace.opacity = 0.7
ete.add_face_to_node(thisFace, node, column=0, position="float")
textF = ete.TextFace(str(size), fsize=12, fgcolor="steelblue")
ete.add_face_to_node(textF, node, column=0, position="aligned")
def ly_basic(node):
if node.is_leaf():
node.img_style['size'] = 0
else:
node.img_style['size'] = 0
node.img_style['shape'] = 'square'
if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
if node.tree_seqtype == "nt":
node.img_style["bgcolor"] = "#CFE6CA"
ntF = TextFace("nt",
fsize=6,
fgcolor='#444',
ftype='Helvetica')
add_face_to_node(ntF, node, 10, position="branch-bottom")
if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
node.img_style['size'] = 4
node.img_style['fgcolor'] = "steelblue"
node.img_style['hz_line_width'] = 1
node.img_style['vt_line_width'] = 1
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 range(c, len(TRACKED_CLADES)):
add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
node,
c,
position='aligned')
c += 1
def my_layout_extended(node):
N = TextFace(int(node.numbers), fsize=1) # , tight_text=True)
# N = AttrFace(node.numbers, fsize=1, tight_text=True)
add_face_to_node(N, node, column=1, position="branch-right")
style = NodeStyle()
if node.name == "N0":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N0"]
elif node.name == "N1":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N1"]
elif node.name == "N2":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N2"]
elif node.name == "N3":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N3"]
elif node.name == "N4":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N4"]
elif node.name == "N5":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N5"]
elif node.name == "N6":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N6"]
elif node.name == "N7":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N7"]
elif node.name == "N8":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N8"]
elif node.name == "N9":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N9"]
elif node.name == "N10":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N10"]
elif node.name == "N11":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N11"]
elif node.name == "N12":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N12"]
elif node.name == "N13":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N13"]
elif node.name == "N14":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N14"]
elif node.name == "N15":
style["fgcolor"] = style["hz_line_color"] = color_dictionary["N15"]
node.set_style(style)
def my_layout(node):
#
# add names to all nodes (not just to leaf nodes)
# ete3/test/test_treeview/face_rotation.py
F = TextFace(node.name, tight_text=True)
add_face_to_node(F, node, column=0, position="branch-right")
#
# add branch lengths
# ete3/treeview/qt4_render.py
if not node.is_root():
bl_face = AttrFace("dist",
fsize=8,
ftype="Arial",
fgcolor="black",
formatter="%0.3g")
#
# This is a failed attempt to center the branch length text on the branch.
#a = 1 # 0 left, 1 center, 2 right
#bl_face.hz_align = a
#bl_face.vt_align = a
#add_face_to_node(bl_face, node, column=0, aligned=True, position="branch-top")
add_face_to_node(bl_face, node, column=0, position="branch-top")
#
# I guess we also have to explicitly add the alignment column
# if we are overriding the layout function.
# ete3/treeview/layouts.py : phylogeny(node)
if hasattr(node, 'sequence'):
seq_face = SequenceFace(node.sequence, seqtype='nt', fsize=13)
seq_face.margin_left = 4
add_face_to_node(seq_face, node, column=1, aligned=True)
def my_layout(node):
#
# add names to all nodes (not just to leaf nodes)
# ete3/test/test_treeview/face_rotation.py
F = TextFace(node.name, tight_text=True)
add_face_to_node(F, node, column=0, position="branch-right")
#
# add branch lengths
# ete3/treeview/qt4_render.py
if not node.is_root():
bl_face = AttrFace("dist", fsize=8, ftype="Arial",
fgcolor="black", formatter="%0.3g")
#
# This is a failed attempt to center the branch length text on the branch.
#a = 1 # 0 left, 1 center, 2 right
#bl_face.hz_align = a
#bl_face.vt_align = a
#add_face_to_node(bl_face, node, column=0, aligned=True, position="branch-top")
add_face_to_node(bl_face, node, column=0, position="branch-top")
#
# I guess we also have to explicitly add the alignment column
# if we are overriding the layout function.
# ete3/treeview/layouts.py : phylogeny(node)
if hasattr(node, 'sequence'):
seq_face = SequenceFace(node.sequence, seqtype='nt', fsize=13)
seq_face.margin_left = 4
add_face_to_node(seq_face, node, column=1, aligned=True)
def leaf_style(node, seqmeta, tp_colors, highlight_node=None):
name = node.name + " (mf={}) ".format(round(float(seqmeta['mut_freq']), 3))
F = ete3.faces.TextFace(name, fsize=9)
ete3.add_face_to_node(F, node, column=1, position='branch-right')
## Style the node with color corresponding to timepoint
nstyle = ete3.NodeStyle()
#if node.name == highlight_node:
#nstyle['fgcolor'] = 'brown'
#else:
#nstyle['fgcolor'] = tp_colors[seqmeta['timepoint']]
nstyle['size'] = 0
node.set_style(nstyle)
# Style the node with color corresponding to timepoint
if False:
nstyle = ete3.NodeStyle()
if node.name == highlight_node:
nstyle['fgcolor'] = 'brown'
else:
nstyle['fgcolor'] = tp_colors[seqmeta['timepoint']]
nstyle['size'] = 14
node.set_style(nstyle)
timepoints = filter(
lambda x: x,
seqmeta.get('cluster_timepoints', seqmeta['timepoints']).split(':'))
duplicities = [
int(n)
for n in seqmeta.get('cluster_timepoint_multiplicities',
seqmeta['timepoint_multiplicities']).split(':')
if n
]
multiplicity = int(
seqmeta.get('cluster_multiplicity', seqmeta['multiplicity']))
percents = [d * 100 / multiplicity for d in duplicities]
colors = [tp_colors[t] for t in timepoints]
pie_node = ete3.PieChartFace(percents,
width=scale_node(multiplicity),
height=scale_node(multiplicity),
colors=colors,
line_color='black')
ete3.add_face_to_node(pie_node, node, column=0)
def layout(node):
""" layout for ete2 tree plotting fig """
if node.is_leaf():
nameF = ete3.TextFace(node.name, tight_text=False,
fgcolor="#262626", fsize=8)
ete3.add_face_to_node(nameF, node, column=0, position="aligned")
node.img_style["size"] = 0
else:
if not node.is_root():
node.img_style["size"] = 0
node.img_style["shape"] = 'square'
node.img_style["fgcolor"] = "#262626"
if "quartets_total" in node.features:
ete3.add_face_to_node(ete2.PieChartFace(
percents=[float(node.quartets_sampled_prop),
100-float(node.quartets_sampled_prop)],
width=15, height=15, colors=PIECOLORS),
node, column=0, position="float-behind")
if "bootstrap" in node.features:
ete3.add_face_to_node(ete2.AttrFace(
"bootstrap", fsize=7, fgcolor='red'),
node, column=0, position="branch-top")
else:
node.img_style["size"] = 0
if node.is_root():
node.img_style["size"] = 0
node.img_style["shape"] = 'square'
node.img_style["fgcolor"] = "#262626"
def my_layout(node):
seqmeta = annotations.get(node.name)
# handle leaves
if seqmeta and not re.compile("naive").match(node.name):
leaf_style(node, seqmeta, tp_colors, highlight_node)
# Deal with naive and true internal nodes
else:
# Have to set all node sizes to 0 or we end up distorting the x-axis
nstyle = ete3.NodeStyle()
nstyle['size'] = 0
node.set_style(nstyle)
# Highlight just those nodes in the seedlineage which have nonzero branch lengths, or bad things
if node in seed_lineage and node.dist > 0:
position = "float"
# Note; we use circleface instead of node style to avoid borking the x-axis
circle_face = ete3.CircleFace(radius=5,
color='brown',
style="circle")
ete3.add_face_to_node(circle_face,
node,
column=0,
position=position)
def my_layout(node):
N = TextFace(node.numbers, tight_text=True)
add_face_to_node(N, node, column=1, position="branch-right")
style = NodeStyle()
if node.name == "N0":
style["fgcolor"] = style["hz_line_color"] = "red"
elif node.name == "N1":
style["fgcolor"] = style["hz_line_color"] = "lime"
elif node.name == "N2":
style["fgcolor"] = style["hz_line_color"] = "cyan"
elif node.name == "N3":
style["fgcolor"] = style["hz_line_color"] = "plum"
elif node.name == "N4":
style["fgcolor"] = style["hz_line_color"] = "lightsalmon"
elif node.name == "N5":
style["fgcolor"] = style["hz_line_color"] = "indigo"
elif node.name == "N6":
style["fgcolor"] = style["hz_line_color"] = "royalblue"
elif node.name == "N7":
style["fgcolor"] = style["hz_line_color"] = "olive"
node.set_style(style)
def custom_layout(node):
if node.is_leaf():
aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=14)
add_face_to_node(aligned_name_face, node, column=2, position='aligned')
name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
add_face_to_node(name_face, node, column=2, position='branch-right')
node.img_style['size'] = 0
else:
node.img_style['size'] = 4
node.img_style['shape'] = 'square'
if node.name:
name_face = TextFace(node.name, fgcolor='grey', fsize=10)
name_face.margin_bottom = 2
add_face_to_node(name_face, node, column=0, position='branch-top')
if node.support:
support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
add_face_to_node(support_face, node, column=0, position='branch-bottom')
def rotation_layout(node):
if node.is_leaf():
if node.name == 'X':
F = TextFace(node.name, tight_text=True, fgcolor='Blue')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
elif node.name == 'Y':
F = TextFace(node.name, tight_text=True, fgcolor='Red')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
elif node.name == 'A':
F = TextFace("")
add_face_to_node(F, node, column=0, position="branch-right")
else:
F = TextFace(node.name, tight_text=True, fgcolor='Green')
F.rotation = 90
add_face_to_node(F, node, column=0, position="branch-right")
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_supports(node):
if not node.is_leaf() and node.up:
supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred')
add_face_to_node(supFace, node, column=0, position='branch-top')
def layout(node):
if node.is_leaf():
seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
add_face_to_node(seqFace, node, 0, position="aligned")
def custom_layout(self,node):
if node.is_leaf():
aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=12)
aligned_name_face.margin_top = 5
aligned_name_face.margin_right = 5
aligned_name_face.margin_left = 5
aligned_name_face.margin_bottom = 5
aligned_name_face.hz_align = 0 #0 = left, 1 = center, 2 = right
add_face_to_node(aligned_name_face, node, column=2, position='aligned')
#name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
#name_face.margin_top = 3
#name_face.margin_right = 3
#name_face.margin_left = 3
#name_face.margin_bottom = 3
#add_face_to_node(name_face, node, column=2, position='branch-right')
node.img_style['size'] = 0
#---------------------------------------------
#displaying extra categorical and numeric data
if (node.name in self._tip2info):
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_data = self._tip2info[node.name][headerIndex]
if isinstance( extra_data, ( int, float ) ):
extra_face = BarChartFace([extra_data], width=100,height=25,colors=[self._tip2color[node.name][headerIndex]],labels=[dataheader],min_value=0.0,max_value=self._tip_max)
else:
extra_face = TextFace(extra_data, fsize=11, fgcolor='black')
extra_face.background.color = self._tip2color[node.name][headerIndex]
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
#add_face_to_node(extra_face, node, column=column_no, aligned = True, position='branch-right')
column_no += 1
else:
#print "No data available"
column_no = 3
for headerIndex, dataheader in enumerate(self._tip2headers):
extra_face = TextFace("No data available", fsize=10, fgcolor='black')
extra_face.margin_left = 5
extra_face.margin_top = 5
extra_face.margin_right = 5
extra_face.margin_bottom = 5
add_face_to_node(extra_face, node, column=column_no, position='aligned')
column_no += 1
image_col_no = column_no
#----------------------------------------------
if (node.name in self._img_chk_list):
if self._img_data_dic[node.name] is not None:
img_face = ImgFace(self._img_data_dic[node.name], is_url=True)
#img_face = ImgFace(self._tip2info[node.name][0], is_url=True)
#img_path = os.path.join("file:///home/tayeen/TayeenFolders/TreeViewer/WebTreeApp/newplugin_test/data/", "328653.jpg")
#img_face = ImgFace(img_path, is_url=True)
img_face.margin_top = 10
img_face.margin_right = 10
img_face.margin_left = 10
img_face.margin_bottom = 10
#add_face_to_node(img_face, node, column=3, position='branch-right')
#add_face_to_node(img_face, node, column=3, aligned= True, position='branch-right')
else:
img_path = os.path.join("file://"+image_path, "ina.jpg")
img_face = ImgFace(img_path, is_url=True)
#add_face_to_node(img_face, node, column=5, position='branch-right')
add_face_to_node(img_face, node, column=image_col_no, position='aligned')
else: #node is not a leaf
node.img_style['size'] = 4
node.img_style['shape'] = 'square'
if node.name and self._custom_options["draw_internal"]:
name_face = TextFace(node.name, fgcolor='grey', fsize=10)
name_face.margin_top = 4
name_face.margin_right = 4
name_face.margin_left = 4
name_face.margin_bottom = 4
add_face_to_node(name_face, node, column=0, position='branch-top')
if node.name in self._node2label:
label_face = TextFace(self._node2label[node.name], fgcolor='DarkGreen', fsize=10)
label_face.margin_top = 4
label_face.margin_right = 4
label_face.margin_left = 4
label_face.margin_bottom = 4
add_face_to_node(label_face, node, column=0, position="branch-top")
if node.support and self._custom_options["draw_support"]:
support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
support_face.margin_top = 4
support_face.margin_right = 4
support_face.margin_left = 4
support_face.margin_bottom = 4
add_face_to_node(support_face, node, column=0, position='branch-bottom')
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
# 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
#parse all nodes features
if hasattr(node, "bh_bgcolor"):
node.img_style["bgcolor"]= node.bh_bgcolor
if hasattr(node, "bh_size"):
node.img_style["size"]= node.bh_size
if hasattr(node, "lh_color"):
node.img_style['hz_line_color'] = node.lh_color
node.img_style["vt_line_color"] = node.lh_color
if hasattr(node, "lh_width"):
node.img_style['hz_line_width'] = node.lh_width
node.img_style['vt_line_width'] = node.lh_width
if hasattr(node, "lh_width") and hasattr(node, "lh_color"):
for n in node.iter_descendants():
n.img_style['hz_line_color'] = node.lh_color
n.img_style["vt_line_color"] = node.lh_color
n.img_style['hz_line_width'] = node.lh_width
n.img_style['vt_line_width'] = node.lh_width
