def draw(self,
file,
colors,
color_internal_nodes=True,
legend_labels=(),
show_branch_support=True,
show_scale=True,
legend_scale=1,
mode="c",
neighbours=None,
neighbours_block=None):
max_color = len(colors)
used_colors = set()
for node in self.tree.traverse():
if not (color_internal_nodes or node.is_leaf()): continue
color = colors[min(node.color, max_color - 1)]
node.img_style['bgcolor'] = color
used_colors.add(color)
ts = TreeStyle()
ts.mode = mode
ts.scale = self.scale
# Disable the default tip names config
ts.show_leaf_name = False
ts.show_branch_support = show_branch_support
# ts.branch_vertical_margin = 20
ts.show_scale = show_scale
cur_max_color = max(v.color for v in self.tree.traverse())
current_colors = colors[0:cur_max_color + 1]
for i, (label, color_) in enumerate(zip(legend_labels,
current_colors)):
if color_ not in used_colors: continue
rf = RectFace(20 * legend_scale, 16 * legend_scale, color_, color_)
rf.inner_border.width = 1
rf.margin_right = 14
rf.margin_left = 14
tf = TextFace(label, fsize=26 * legend_scale)
tf.margin_right = 14
ts.legend.add_face(rf, column=0)
ts.legend.add_face(tf, column=1)
if neighbours:
old_tree = self.tree.copy()
self.draw_neighbours(neighbours, neighbours_block)
self.tree.render(file, w=1000, tree_style=ts)
if neighbours:
self.tree = old_tree
def draw_tree(tree, conf, outfile):
try:
from ete3 import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace,
SequenceFace, random_color, SeqMotifFace)
except ImportError as e:
print(e)
return
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_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_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 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_full_alg(node):
pass
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)
TRACKED_CLADES = ["Eukaryota", "Viridiplantae", "Fungi",
"Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta",
"Amoebozoa", "Crypthophyta", "Bacteria",
"Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
"Gammaproteobacteria",]
# ["Opisthokonta", "Apicomplexa"]
colors = random_color(num=len(TRACKED_CLADES), s=0.45)
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])
NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')
LABEL_START_COL = 10
ALG_START_COL = 40
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.scale = 160
ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]
MIXED_RES = set()
MAX_SEQ_LEN = 0
NPR_TREES = []
for n in tree.traverse():
if hasattr(n, "tree_seqtype"):
MIXED_RES.add(n.tree_seqtype)
if hasattr(n, "tree_type"):
NPR_TREES.append(n.tree_type)
seq = getattr(n, "sequence", "")
MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)
if MAX_SEQ_LEN:
ALG_SCALE = min(1, 1000./MAX_SEQ_LEN)
ts.layout_fn.append(ly_block_alg)
if len(NPR_TREES) > 1:
rF = RectFace(4, 4, "steelblue", "steelblue")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" NPR node"), 1)
ts.legend_position = 3
if len(MIXED_RES) > 1:
rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
ts.legend_position = 3
try:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
a = tree.search_nodes(species='Dictyostelium discoideum')[0]
b = tree.search_nodes(species='Chondrus crispus')[0]
#out = tree.get_common_ancestor([a, b])
#out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
tree.set_outgroup(out)
tree.swap_children()
except Exception:
pass
tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
def draw_tree(tree, conf, outfile):
try:
from ete3 import (add_face_to_node, AttrFace, TextFace, TreeStyle,
RectFace, CircleFace, SequenceFace, random_color,
SeqMotifFace)
except ImportError as e:
print(e)
return
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_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_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 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_full_alg(node):
pass
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)
TRACKED_CLADES = [
"Eukaryota",
"Viridiplantae",
"Fungi",
"Alveolata",
"Metazoa",
"Stramenopiles",
"Rhodophyta",
"Amoebozoa",
"Crypthophyta",
"Bacteria",
"Alphaproteobacteria",
"Betaproteobacteria",
"Cyanobacteria",
"Gammaproteobacteria",
]
# ["Opisthokonta", "Apicomplexa"]
colors = random_color(num=len(TRACKED_CLADES), s=0.45)
lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])
NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')
LABEL_START_COL = 10
ALG_START_COL = 40
ts = TreeStyle()
ts.draw_aligned_faces_as_table = False
ts.draw_guiding_lines = False
ts.show_leaf_name = False
ts.show_branch_support = False
ts.scale = 160
ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]
MIXED_RES = set()
MAX_SEQ_LEN = 0
NPR_TREES = []
for n in tree.traverse():
if hasattr(n, "tree_seqtype"):
MIXED_RES.add(n.tree_seqtype)
if hasattr(n, "tree_type"):
NPR_TREES.append(n.tree_type)
seq = getattr(n, "sequence", "")
MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)
if MAX_SEQ_LEN:
ALG_SCALE = min(1, 1000. / MAX_SEQ_LEN)
ts.layout_fn.append(ly_block_alg)
if len(NPR_TREES) > 1:
rF = RectFace(4, 4, "steelblue", "steelblue")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" NPR node"), 1)
ts.legend_position = 3
if len(MIXED_RES) > 1:
rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
rF.margin_right = 10
rF.margin_left = 10
ts.legend.add_face(rF, 0)
ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
ts.legend_position = 3
try:
tree.set_species_naming_function(spname)
annotate_tree_with_ncbi(tree)
a = tree.search_nodes(species='Dictyostelium discoideum')[0]
b = tree.search_nodes(species='Chondrus crispus')[0]
#out = tree.get_common_ancestor([a, b])
#out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
tree.set_outgroup(out)
tree.swap_children()
except Exception:
pass
tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile + '.svg', tree_style=ts, w=170, units='mm', dpi=150)
tree.render(outfile + '.pdf', tree_style=ts, w=170, units='mm', dpi=150)
def nodeLayoutFunc(node):
taxid = int(node.name)
if taxid in taxidsToKeep:
taxGroupName = ncbiTaxa.get_taxid_translator(
[taxid]
)[taxid] # There has to be an easier way to look up names...
row = None
rangeRows = None
print(len(ranges))
if (len(ranges) == 1):
row = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'] == ranges[0])]
assert (len(row) == len(ranges))
elif len(ranges) > 1:
row = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'] == 0)]
assert (len(row) == 1)
rangeRows = df[(df['ExplanatoryVar'] == var)
& (df['TaxGroup'] == taxid) &
(df['Range'].isin(set(ranges)))]
else:
assert (False)
overallPval = float(row['Pvalue'].values[0])
name = TextFace("%s" % taxGroupName,
fsize=baseFontSize * 2.5)
name.tight_text = True
name.margin_left = 20
name.margin_right = 0
name.margin_top = 40
name.margin_bottom = 12
faces.add_face_to_node(name, node, column=0)
#print(rangeRows)
# For each range to be included in this plot, add a bar
for rangeId in ranges:
#print("rangeId = %s" % (rangeId))
rowForThisRange = None
if len(ranges) == 1:
rowForThisRange = row
else:
rowForThisRange = rangeRows[rangeRows['Range'] ==
rangeId]
assert (len(rowForThisRange) == 1)
# Extract p-value and "effect-size" (signed R^2)
effectSize = float(
rowForThisRange['EffectSize'].values[0])
pval = float(rowForThisRange['Pvalue'].values[0])
# Set bar-graph color and significance markers
barColor = ""
significanceMarker = ""
if (pval < significanceLevel):
significanceMarker = " %s" % unichr(0x2731)
if effectSize < 0:
barColor = "#1133ff"
else:
barColor = "#ff3311"
else: # not significant
if effectSize < 0:
barColor = "#b0b0f0"
else:
barColor = "#ccb090"
# Add the minus sign if needed
signChar = ""
if effectSize < 0:
signChar = unichr(
0x2212
) # minus sign (more legible than a hypen...)
v = RectFace(width=abs(effectSize) * barScale,
height=baseFontSize * 3.5,
fgcolor=barColor,
bgcolor=barColor,
label={
"text":
"%s%.2g %s" %
(signChar, abs(effectSize),
significanceMarker),
"fontsize":
baseFontSize * 1.8,
"color":
"black"
})
#v.rotation = -90
v.margin_top = 1
v.margin_left = 30
v.margin_right = 8
v.margin_bottom = 12
faces.add_face_to_node(v, node, column=0)
details = TextFace(
"N=%d" % row['NumSpecies'], fsize=baseFontSize *
1.5) #, fsize=baseFontSize) #, fstyle="italic")
details.background.color = "#dfdfdf"
details.margin_left = 6
details.margin_right = 20
#details.margin_top=5
#details.margin_bottom=0
faces.add_face_to_node(details, node, column=1)
nstyle = NodeStyle()
nstyle["size"] = 0
node.set_style(nstyle)