def get_tree(tree1, abundance):
for n in tree1.iter_leaves():
face1 = CircleFace(abundance[n.name][0],
abundance[n.name][1],
style='sphere')
face2 = TextFace(n.name,
ftype='Verdana',
fsize=10,
fgcolor='black',
penwidth=0,
fstyle='normal',
tight_text=False,
bold=False)
face1.opacity = 0.9
n.add_face(face1, column=0)
n.add_face(
face2, column=0,
position="branch-right") #branch-top branch-bottom branch-right
tree1.ladderize()
ts = TreeStyle()
ts.mode = 'r'
ts.scale = scale1
ts.show_leaf_name = False
return tree1, ts
def plot_variance(tree,path,aa):
#cycle through the nodes and add a variance attribute to each node postorder, so we start with the
#children that have W attribute and recursively create this attribute as we are traversing through the tree
all_means=[]
for node in tree.traverse(strategy="postorder"):
if not(node.is_leaf()):
children=node.children
variance=[]
for i in range(len(children)):
aa_feat = getattr(children[i], aa)
variance.append(aa_feat)
# variance requires at least two data points, in case there is only one sequence or node
if len(variance)==1:
node.add_feature(aa+"_var",0)
node.add_feature(aa+"", np.mean(variance))
else:
node.add_feature(aa+"_var",statistics.variance(variance))
node.add_feature(aa+"", np.mean(variance))
all_means.append(getattr(node, aa+""))
#plot without sequences (create new tree with cut leave and )
new_tree=tree.copy()
maximum=max(all_means)
minimum=min(all_means)
#for node in new_tree.traverse(strategy="preorder"):
ts = TreeStyle()
ts.mode="c"
for node in new_tree.traverse():
if node.is_leaf():
node.detach()
else:
nstyle = NodeStyle()
nstyle["bgcolor"]="#"+rgb_to_hex(red_gradient(minimum,maximum,(getattr(node, aa+""))))
node.add_face(TextFace(getattr(node,aa+"")), column=0, position = "branch-right")
node.set_style(nstyle)
new_tree.render(path, w=1400, units="mm", tree_style=ts)
def get_example_tree():
# Set dashed blue lines in all leaves
nst1 = NodeStyle()
nst1["bgcolor"] = "LightSteelBlue"
nst2 = NodeStyle()
nst2["bgcolor"] = "Moccasin"
nst3 = NodeStyle()
nst3["bgcolor"] = "DarkSeaGreen"
nst4 = NodeStyle()
nst4["bgcolor"] = "Khaki"
t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
for n in t.traverse():
n.dist = 0
n1 = t.get_common_ancestor("a1", "a2", "a3")
n1.set_style(nst1)
n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
n2.set_style(nst2)
n3 = t.get_common_ancestor("c1", "c2", "c3")
n3.set_style(nst3)
n4 = t.get_common_ancestor("b3", "b4")
n4.set_style(nst4)
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
ts.mode = "c"
ts.root_opening_factor = 1
return t, ts
def get_example_tree():
# Set dashed blue lines in all leaves
nst1 = NodeStyle()
nst1["bgcolor"] = "LightSteelBlue"
nst2 = NodeStyle()
nst2["bgcolor"] = "Moccasin"
nst3 = NodeStyle()
nst3["bgcolor"] = "DarkSeaGreen"
nst4 = NodeStyle()
nst4["bgcolor"] = "Khaki"
t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
for n in t.traverse():
n.dist = 0
n1 = t.get_common_ancestor("a1", "a2", "a3")
n1.set_style(nst1)
n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
n2.set_style(nst2)
n3 = t.get_common_ancestor("c1", "c2", "c3")
n3.set_style(nst3)
n4 = t.get_common_ancestor("b3", "b4")
n4.set_style(nst4)
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
ts.mode = "c"
ts.root_opening_factor = 1
return t, ts
def get_example_tree():
# Set dashed blue lines in all leaves
nst1 = NodeStyle()
nst1["bgcolor"] = "LightSteelBlue"
nst2 = NodeStyle()
nst2["bgcolor"] = "Moccasin"
nst3 = NodeStyle()
nst3["bgcolor"] = "DarkSeaGreen"
nst4 = NodeStyle()
nst4["bgcolor"] = "Khaki"
t = Tree("( 🌲,( 🥑,(( 🌷, ( 🌴, ( 🍌, ( 🍍, ( 🌽, ( 🎋, 🌾 )))))),(( 🍇, ((( 🥜, ☘️), ((( 🌹, 🍓 ), (( 🍎, 🍐 ), ( 🍑, (🌸, 🍒) ))), ( 🌰, ( 🎃, ( 🍉, ( 🥒, 🍈)))))), (( 🌺, 🥦 ), (( 🍊, 🍋 ), ( 🍁, 🥭))))),( 🌵, ( 🥝, (( 🍠, ( 🌶️, (🍆, ( 🥔, 🍅)))), ( 🥕,( 🥬, ( 🌻, 🌼)))))))));")
for n in t.traverse():
n.dist = 0
n1 = t.get_common_ancestor("a1", "a2", "a3")
n1.set_style(nst1)
n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
n2.set_style(nst2)
n3 = t.get_common_ancestor("c1", "c2", "c3")
n3.set_style(nst3)
n4 = t.get_common_ancestor("b3", "b4")
n4.set_style(nst4)
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
ts.mode = "c"
ts.root_opening_factor = 1
return t, ts
def buble_tree():
built = False
while not built:
try:
# Random tree
t = ncbi.get_topology(idtaxa, intermediate_nodes=True)
# Some random features in all nodes
for node,weigh in zip(t,weighs):
node.add_features(weight=weigh)
# 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 = True
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
return t, ts
built = True
except KeyError as e:
taxid_not_found = int(e.args[0])
idtaxa.remove(taxid_not_found)
print("the following IDs were not found in NCBI taxonomy database:" + str(taxid_not_found))
pass
def plot_trees(tree_fn, output_fn):
""" Plot a tree """
os.environ['QT_QPA_PLATFORM'] = 'offscreen'
style = TreeStyle()
style.mode = "c"
style.show_leaf_name = True
# Set Node Styles
rstyle = NodeStyle()
rstyle["shape"] = "sphere"
rstyle["size"] = 15
rstyle["fgcolor"] = "blue"
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 0
sstyle = NodeStyle()
sstyle["shape"] = "sphere"
sstyle["size"] = 15
sstyle["fgcolor"] = "red"
#Create the tree object
ct = Tree(tree_fn)
for n in ct.traverse():
if n.name == "Wuhan" or n.name == "Wuhan|402124":
n.set_style(rstyle)
elif n.name == "Sample":
n.set_style(sstyle)
elif not n.is_leaf():
n.set_style(nstyle)
#Draw the tree and write to a file
ct.render(output_fn, tree_style=style)
def get_example_tree(tree, color_dict=None, annot_dict=None, col=None):
used_colours = set()
for n in tree.traverse():
if n.is_leaf():
if n.name in annot_dict:
n.img_style["bgcolor"] = color_dict[annot_dict[n.name]]
used_colours.add(annot_dict[n.name])
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
ts.mode = "c"
# ts.arc_start = -180 # 0 degrees = 3 o'clock
# ts.arc_span = 180
# ts.root_opening_factor = 1
# print (used_colours)
for k,v in color_dict.items():
# Check that the specific colour was actually present in the tree we're annotating
if k in used_colours:
ts.legend.add_face(CircleFace(100, v), column=0)
ts.legend.add_face(TextFace(k, fsize=50), column=1)
# Add title
ts.title.add_face(TextFace("Colouring tips on " + col, fsize=100), column=0)
return tree, ts
def show_tree(experiment_folder):
model = MDPD.Hierachical_MDPD(1)
model.load(os.path.join(experiment_folder, 'model.p'))
width, depth = model.width, model.depth
root = Tree()
cache = [(0, root)]
for i in range(depth + 1):
foo = []
for idx, node in cache:
paren = int((idx - 1) / width)
kid = idx - paren * width
face = faces.ImgFace(os.path.join(experiment_folder, 'images', '{}_{}_{}.png'.format(idx, paren, kid)))
node.add_face(face, 0)
if i < depth:
for k in range(width):
foo.append((idx * width + k + 1, node.add_child()))
cache = foo
ts = TreeStyle()
ts.mode = "c"
root.render(os.path.join(experiment_folder, 'images', 'tree_plot.png'), tree_style=ts)
return root
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 = Tree(
"(((yessefk),(ad, tuɣal),((teqbaylit),(d,(tutlayt,tunṣibt)))),(((win,yebɣan), (taqbaylit)),(((ad,yissin, (tira,-s))))),(((win,yebɣan), (taqbaylit)),(((yugar) , (ucerrig)), (tafawet))));"
)
# 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(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():
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 add_labels_n_colors_2_tree(tree_path, refseq_2_entropy, colors, feature, out):
"""
add entropy measurement to a tree and color it's leaves
:param tree_path: a path to a tree
:param refseq_2_entropy: a data base with entropy values for each refseq id
:param out: output directory path to save the results
:return: a tree with colors and entropy labels
"""
print(tree_path)
str_tree = tree_2_string(tree_path)
if str_tree == '':
return
tree = Tree(str_tree)
# get all refseq ids in the tree and all corresponding entropy values
all_leaves = []
for node in tree:
if node.is_leaf():
all_leaves.append(node.name)
#all_values = refseq_2_entropy[refseq_2_entropy['refseq_id'].isin(all_leaves)]['entropy_5'].values
all_values = refseq_2_entropy[feature].values
num_leaves = len(all_leaves)
# create a gradient color bar
#colors = linear_gradient("#DC9221", "#33C193", n=num_leaves)
#mapping = value_2_color(all_values, colors['hex'])
mapping = value_2_color(all_values, colors['hex'])
for node in tree:
if node.is_leaf():
value = refseq_2_entropy[refseq_2_entropy['refseq_id'] == node.name.split('.')[0]][feature].values[0]
virus_name = refseq_2_entropy[refseq_2_entropy['refseq_id'] == node.name.split('.')[0]]['virus_name'].values[0]
# change virus name
node.name = virus_name
c = mapping[str(value)]
node.add_feature("label", value)
label_face = TextFace(node.label, fgcolor=c, fsize=22)
node.add_face(label_face, column=0, position='branch-right')
family = os.path.basename(tree_path).split('.')[0]
ts = TreeStyle()
ts.mode = 'c'
ts.scale = 5
# Disable the default tip names config
ts.show_leaf_name = True
ts.show_scale = True
ts.show_branch_length = True
ts.title.add_face(TextFace("{} values for {}".format(feature, family), fsize=20), column=0)
# Draw Tree
tree.render(os.path.join(out, '{}_{}_tree.pdf'.format(family, feature)), dpi=300, tree_style=ts)
def render_tree(T, out):
ts = TreeStyle()
ts.show_leaf_name = False
ts.mode = "c"
ts.scale = 200
ts.show_scale = False
T.render(out, tree_style=ts, layout=layout_black_circles)
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 plot_newick(aug_cluster_list, mode='c', db=-1):
circular_style = TreeStyle()
circular_style.mode = mode # draw tree in circular mode
circular_style.scale = 20
circular_style.arc_span = 360
if db > 0:
newick = convert_to_newick_db(aug_cluster_list,
len(aug_cluster_list) - 1, db)
circular_style.mode = mode
else:
newick = convert_to_newick(aug_cluster_list, len(aug_cluster_list) - 1)
newick = newick + ':0;'
t = Tree(newick, format=1)
t.show(tree_style=circular_style)
if False:
t.render('tree3.png', w=100, units='in', tree_style=circular_style)
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 create_tree_style():
ts = TreeStyle()
ts.title.add_face(TextFace("Randomly pruned data", fsize=20), column=0)
ts.layout_fn = remove_blue_dots
ts.mode = "c"
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
return ts
def tree_style() -> TreeStyle:
style = TreeStyle()
style.mode = "c" # draw tree in circular mode
# style.scale = 20
# style.branch_vertical_margin = 15
style.root_opening_factor = 0.04
style.show_leaf_name = False
style.show_branch_length = False
style.show_branch_support = False
return style
def balanceplot(balances, tree,
layout=None,
mode='c'):
""" Plots balances on tree.
Parameters
----------
balances : np.array
A vector of internal nodes and their associated real-valued balances.
The order of the balances will be assumed to be in level order.
tree : skbio.TreeNode
A strictly bifurcating tree defining a hierarchical relationship
between all of the features within `table`.
layout : function, optional
A layout for formatting the tree visualization. Must take a
`ete.tree` as a parameter.
mode : str
Type of display to show the tree. ('c': circular, 'r': rectangular).
Note
----
The `tree` is assumed to strictly bifurcating and
whose tips match `balances.
See Also
--------
TreeNode.levelorder
"""
# The names aren't preserved - let's pray that the topology is consistent.
ete_tree = Tree(str(tree))
# Some random features in all nodes
i = 0
for n in ete_tree.traverse():
if not n.is_leaf():
n.add_features(weight=balances[-i])
i += 1
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
if layout is None:
ts.layout_fn = default_layout
else:
ts.layout_fn = layout
# Draw a tree
ts.mode = mode
# 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 ete_tree, ts
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 ete_draw(t,fname=None,title='',mode='r',outfile='ete_tree.png'):
from ete3 import Tree, TreeStyle, Phyloxml, TextFace
t.children
ts = TreeStyle()
#ts.branch_vertical_margin = 10
ts.show_scale=False
ts.scale = 800
ts.show_leaf_name = False
ts.mode = mode
ts.title.add_face(TextFace(title, fsize=20), column=0)
t.render(outfile,dpi=300,h=800,tree_style=ts)
return ts
def _get_motif_tree(tree, data, circle=True, vmin=None, vmax=None):
try:
from ete3 import Tree, NodeStyle, TreeStyle
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
t = Tree(tree)
# Determine cutoff for color scale
if not (vmin and vmax):
for i in range(90, 101):
minmax = np.percentile(data.values, i)
if minmax > 0:
break
if not vmin:
vmin = -minmax
if not vmax:
vmax = minmax
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap="RdBu_r")
m = 25 / data.values.max()
for node in t.traverse("levelorder"):
val = data[[l.name for l in node.get_leaves()]].values.mean()
style = NodeStyle()
style["size"] = 0
style["hz_line_color"] = to_hex(mapper.to_rgba(val))
style["vt_line_color"] = to_hex(mapper.to_rgba(val))
v = max(np.abs(m * val), 5)
style["vt_line_width"] = v
style["hz_line_width"] = v
node.set_style(style)
ts = TreeStyle()
ts.layout_fn = _tree_layout
ts.show_leaf_name = False
ts.show_scale = False
ts.branch_vertical_margin = 10
if circle:
ts.mode = "c"
ts.arc_start = 180 # 0 degrees = 3 o'clock
ts.arc_span = 180
return t, ts
def _get_motif_tree(tree, data, circle=True, vmin=None, vmax=None):
try:
from ete3 import Tree, NodeStyle, TreeStyle
except ImportError:
print("Please install ete3 to use this functionality")
sys.exit(1)
t = Tree(tree)
# Determine cutoff for color scale
if not(vmin and vmax):
for i in range(90, 101):
minmax = np.percentile(data.values, i)
if minmax > 0:
break
if not vmin:
vmin = -minmax
if not vmax:
vmax = minmax
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap="RdBu_r")
m = 25 / data.values.max()
for node in t.traverse("levelorder"):
val = data[[l.name for l in node.get_leaves()]].values.mean()
style = NodeStyle()
style["size"] = 0
style["hz_line_color"] = to_hex(mapper.to_rgba(val))
style["vt_line_color"] = to_hex(mapper.to_rgba(val))
v = max(np.abs(m * val), 5)
style["vt_line_width"] = v
style["hz_line_width"] = v
node.set_style(style)
ts = TreeStyle()
ts.layout_fn = _tree_layout
ts.show_leaf_name= False
ts.show_scale = False
ts.branch_vertical_margin = 10
if circle:
ts.mode = "c"
ts.arc_start = 180 # 0 degrees = 3 o'clock
ts.arc_span = 180
return t, ts
def Generate_CircleTree(treeData, output_path):
# Define output file name and its path
file_name = "circle_tree.png"
out_file = output_path + "/" + file_name
# Build tree & incorporate desired parameters for visualization
t = Tree(treeData)
circular_style = TreeStyle()
circular_style.mode = "c"
circular_style.scale = 20
# Produce/draw output figure: phylogeny
t.render(file_name, w=183, units="mm", tree_style=circular_style)
def get_style():
# 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 = True
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
return ts
def plot_tree(tree, save=False, path=''):
# style
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180
ts.arc_span = 360
#plot tree
if save:
tree.render(file_name=path, tree_style=ts)
tree.show(tree_style=ts)
def plot_taxids(taxids_list, tree_png, tree_nw, tax_db=None):
if tax_db is not None:
ncbi = NCBITaxa(dbfile=tax_db)
else:
ncbi=NCBITaxa()
tree = ncbi.get_topology(taxids_list)
ts = TreeStyle()
ncbi.annotate_tree(tree, taxid_attr="sci_name")
ts.show_leaf_name = False
ts.mode = "c"
ts.layout_fn = layout
tree.render(tree_png, tree_style=ts)
tree.write(format=1, outfile=tree_nw)
def set_default_TreeStyle(tree, draw_nodes):
ts = TreeStyle()
ts.mode = "c"
ts.arc_start = -180
ts.arc_span = 180
ts.root_opening_factor = 1
ts.show_branch_length = False
ts.show_branch_support = True
ts.force_topology = False
ts.show_leaf_name = False
ts.min_leaf_separation = 10
ts.root_opening_factor = 1
ts.complete_branch_lines_when_necessary = True
return ts, tree
def main(args):
# STEP 1: Set up logger
log = logging.getLogger(__name__)
coloredlogs.install(fmt='%(asctime)s [%(levelname)s] %(message)s', level='DEBUG', logger=log)
# STEP 2: Retrieve and/or update localized NCBI Taxonomy database
ncbi = NCBITaxa()
if (time.time() - os.path.getmtime(os.path.join(Path.home(), ".etetoolkit/taxa.sqlite"))) > 604800:
ncbi.update_taxonomy_database()
# STEP 3: Prune species-level tree to family-level
# Step 3.1 Read tree from input file
log.debug("Loading Tree...")
t = Tree(args.infn, format=5)
# STEP 3.2: Add species names to species_set_from_tree set
log.debug("Gathering species(leaf) names...")
species_set_from_tree = set()
for leaf in t.iter_leaves():
species_set_from_tree.add(leaf.name.replace("_"," "))
# STEP 3.3: Assign species to families
log.debug("Constructing dict of species in family...")
species_in_family = get_species_in_family(species_set_from_tree, ncbi)
# STEP 3.4: Prune the tree
log.debug("Pruning Tree to family level...")
prune_to_family(t, species_in_family)
# STEP 4: Calculate counts of species per family and plastid genome entries per family and attach them to the tree leaves
# STEP 4.1: Read plastid genome information from input table
species_list_from_table = get_species_list_from_table(args.tablefn)
# STEP 4.2: Count plastid genome entries per family
log.debug("Counting plastid genome entries per family...")
genome_count_per_family = get_genome_count_per_family(species_list_from_table, species_in_family)
# STEP 4.3: Attach counts to tree leaves
log.debug("Attaching counts to Tree...")
attach_counts_to_tree(t, genome_count_per_family, get_species_count_per_family(species_in_family))
# STEP 5: Set TreeStyle and render tree
ts = TreeStyle()
ts.mode = "c"
ts.draw_guiding_lines = True
ts.show_leaf_name = False
log.debug("Rendering Tree...")
t.render(args.outfn, w=10000, h=10000, tree_style=ts)
def my_tree():
ncbi = NCBITaxa()
my_tree = ncbi.get_topology([54263, 8324, 8323, 8327, 8325, 57571, 323754])
for n in my_tree.traverse():
n.add_features(weight=random.randint(0, 50))
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_branch_length = True
ts.show_branch_support = True
my_tree.get_ascii(attributes=["sci_name", "rank"])
return my_tree, ts
def draw_tree(pstrains, names=False, subset=None):
evol = {x.rstrip() for x in open('input/evolution_experiment.txt')}
tree = get_tree('input/tree.nwk')
strains = {x.name for x in tree.traverse() if x.name != ''}
if subset is None:
subset = strains
evol_tree = {x.name for x in tree.traverse() if x.name in evol}
commensals = {}
for x in strains:
if pstrains[x] == 'Commensal strain':
commensals[x] = colors.cnames['blue']
elif pstrains[x] == 'Pathogenic strain':
commensals[x] = colors.cnames['red']
else:
commensals[x] = colors.cnames['white']
ref = NodeStyle()
ref['fgcolor'] = sns.xkcd_rgb['light red']
inner = NodeStyle()
inner['size'] = 0
for n in tree.traverse():
if not n.is_leaf():
n.set_style(inner)
continue
if n.name not in subset:
continue
if not names:
r = RectFace(10, 3, commensals[n.name], commensals[n.name])
n.add_face(r, 0, position="aligned")
ev = NodeStyle()
ev["fgcolor"] = "black"
ev['size'] = 3
n.set_style(ev)
circular_style = TreeStyle()
circular_style.mode = "c"
if not names:
circular_style.scale = 1300
else:
circular_style.scale = 7300
circular_style.show_leaf_name = names
return tree, circular_style
def render_tree(tree, fname):
# Generates tree snapshot
npr_nodestyle = NodeStyle()
npr_nodestyle["fgcolor"] = "red"
for n in tree.traverse():
if hasattr(n, "nodeid"):
n.set_style(npr_nodestyle)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
ts.mode = "r"
iterface = faces.TextFace("iter")
ts.legend.add_face(iterface, 0)
tree.dist = 0
tree.sort_descendants()
tree.render(fname, tree_style=ts, w=700)
def render_tree(tree, fname):
# Generates tree snapshot
npr_nodestyle = NodeStyle()
npr_nodestyle["fgcolor"] = "red"
for n in tree.traverse():
if hasattr(n, "nodeid"):
n.set_style(npr_nodestyle)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
ts.mode = "r"
iterface = faces.TextFace("iter")
ts.legend.add_face(iterface, 0)
tree.dist = 0
tree.sort_descendants()
tree.render(fname, tree_style=ts, w=700)
def make_plot():
df = pd.read_csv(f'{args.output}/aa_comp.tsv', sep="\t")
df = df.set_index('Taxon')
z = shc.linkage(df, method='ward')
t = distance_matrix2tree(z, df.index.values)
t.write(outfile=f'{args.output}/distance_matrix.tre')
# Basic tree style
ts = TreeStyle()
ts.show_leaf_name = False
ts.mode = "c"
ts.show_scale = False
ts.layout_fn = mylayout
# PDF rendering
t.render(f'{args.output}/aa_comp_calculator.pdf',
w=183,
units="mm",
tree_style=ts)
def visualize(self, group1=None, group2=None):
import matplotlib
import matplotlib.pyplot as plt
# annotate the cluster roots with their fractions
if group1 or group2:
for i, cluster_root in enumerate(self.cluster_roots):
# count downstream conditions in the leafs
datapoints_in_cluster = list(self.nodes2leaves[cluster_root])
cluster_root.add_face(
TextFace(f"Group1: {len(group1)}// Group2:{len(group2)}"),
column=0,
position="branch-right")
def _custom_layout(node):
cmap_cluster = plt.cm.tab10(
np.linspace(0, 1, len(self.cluster_roots)))
cmap_treated = plt.cm.viridis(np.linspace(0, 1, 2))
if node.is_leaf():
c_cluster = matplotlib.colors.rgb2hex(
cmap_cluster[node.clustering, :])
c_treat = matplotlib.colors.rgb2hex(
cmap_treated[node.treated, :])
node.img_style["fgcolor"] = c_treat
node.img_style["bgcolor"] = c_cluster
if 'is_cluster_root' in node.features:
c_cluster = matplotlib.colors.rgb2hex(
cmap_cluster[node.is_cluster_root, :])
node.img_style["bgcolor"] = c_cluster
node.img_style["draw_descendants"] = False
node.add_face(TextFace(f"#data:{node.n_datapoints}"),
column=0,
position="branch-right")
ts = TreeStyle()
ts.mode = "r"
ts.show_leaf_name = False
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 270
ts.layout_fn = _custom_layout
self.tree.show(tree_style=ts)
def get_default_tree_style(color_dict):
ts = TreeStyle()
ts.mode = "c"
# ts.layout_fn = layout
ts.margin_top = 50
ts.margin_bottom = 0
ts.margin_left = 50
ts.margin_right = 50
ts.show_scale = False
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
for p, c in color_dict.iteritems():
ts.legend.add_face(TextFace(" ", fsize=30), column=0)
ts.legend.add_face(CircleFace(10, c), column=1)
ts.legend.add_face(TextFace(" %s" % p, fsize=30), column=2)
legend_margin_line = 5
while legend_margin_line:
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(TextFace(" "), column=2)
legend_margin_line -= 1
ts.legend_position = 3
return ts
def balancetest(table, grouping, tree,
significance_test=None,
layout=None,
normalize=True,
mode='c'):
""" Performs statistical test on ilr balances and plots on tree.
Parameters
----------
table : pd.DataFrame
A 2D matrix of strictly positive values (i.e. counts or proportions)
where the rows correspond to samples and the columns correspond to
features.
grouping : pd.Series
Vector indicating the assignment of samples to groups. For example,
these could be strings or integers denoting which group a sample
belongs to. It must be the same length as the samples in `table`.
The index must be the same on `table` and `grouping` but need not be
in the same order.
tree : skbio.TreeNode
A strictly bifurcating tree defining a hierarchical relationship
between all of the features within `table`
significance_test : function, optional
A statistical significance function to test for significance between
classes. This function must be able to accept at least two 1D
array_like arguments of floats and returns a test statistic and a
p-value, or a single statistic. By default ``scipy.stats.f_oneway``
is used.
layout : function, optional
A layout for formatting the tree visualization. Must take a
`ete.tree` as a parameter.
mode : str
Type of display to show the tree. ('c': circular, 'r': rectangular).
Returns
-------
ete_tree : ete.Tree
ETE tree converted from the `skbio.TreeNode` object
ts : ete.TreeStyle
ETE tree style used for formatting the visualized tree,
with the test statistic plotted on each of the internal nodes.
Note
----
The `skbio.TreeNode` is assumed to strictly bifurcating and
whose tips match `table`. Also, it is assumed that none
of the values in `table` are zero. Replace with a pseudocount
if necessary.
See also
--------
skbio.TreeNode.bifurcate
skbio.stats.composition.ilr
skbio.stats.multiplicative_replacement
scipy.stats.f_oneway
"""
if np.any(table <= 0):
raise ValueError('Cannot handle zeros or negative values in `table`. '
'Use pseudo counts or ``multiplicative_replacement``.'
)
if significance_test is None:
significance_test = scipy.stats.f_oneway
sorted_features = [n.name for n in tree.tips()][::-1]
if len(sorted_features) != len(table.columns):
raise ValueError('The number of tips (%d) in the tree must be equal '
'to the number features in the table (%d).' %
(len(sorted_features), len(table.columns)))
table = table.reindex(columns=sorted_features)
mat, cats = check_table_grouping(table, grouping)
basis, nodes = phylogenetic_basis(tree)
ilr_coords = ilr(mat, basis=basis)
ete_tree = Tree(str(tree))
_cats = set(cats)
i = 0
for n in ete_tree.traverse():
if not n.is_leaf():
diffs = [ilr_coords[(cats == x).values, i] for x in _cats]
stat = significance_test(*diffs)
if len(stat) == 2:
n.add_features(weight=-np.log(stat[1]))
elif len(stat) == 1:
n.add_features(weight=stat)
else:
raise ValueError(
"Too many arguments returned by %s" %
significance_test.__name__)
i += 1
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
if layout is None:
ts.layout_fn = default_layout
else:
ts.layout_fn = layout
# Draw a tree
ts.mode = mode
# 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 ete_tree, ts
def run(args):
if args.text_mode:
from ete3 import Tree
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = Tree(nw)
else:
t = Tree(tfile)
print(t.get_ascii(show_internal=args.show_internal_names,
attributes=args.show_attributes))
return
import random
import re
import colorsys
from collections import defaultdict
from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
add_face_to_node, random_color)
global FACES
if args.face:
FACES = parse_faces(args.face)
else:
FACES = []
# VISUALIZATION
ts = TreeStyle()
ts.mode = args.mode
ts.show_leaf_name = True
ts.tree_width = args.tree_width
for f in FACES:
if f["value"] == "@name":
ts.show_leaf_name = False
break
if args.as_ncbi:
ts.show_leaf_name = False
FACES.extend(parse_faces(
['value:@sci_name, size:10, fstyle:italic',
'value:@taxid, color:grey, size:6, format:" - %s"',
'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
]))
if args.alg:
FACES.extend(parse_faces(
['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
))
if args.heatmap:
FACES.extend(parse_faces(
['value:@name, size:10, pos:aligned, ftype:heatmap']
))
if args.bubbles:
for bubble in args.bubbles:
FACES.extend(parse_faces(
['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
]))
ts.branch_vertical_margin = args.branch_separation
if args.show_support:
ts.show_branch_support = True
if args.show_branch_length:
ts.show_branch_length = True
if args.force_topology:
ts.force_topology = True
ts.layout_fn = lambda x: None
for tindex, tfile in enumerate(args.src_tree_iterator):
#print tfile
if args.raxml:
nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
t = PhyloTree(nw)
else:
t = PhyloTree(tfile)
if args.alg:
t.link_to_alignment(args.alg, alg_format=args.alg_format)
if args.heatmap:
DEFAULT_COLOR_SATURATION = 0.3
BASE_LIGHTNESS = 0.7
def gradient_color(value, max_value, saturation=0.5, hue=0.1):
def rgb2hex(rgb):
return '#%02x%02x%02x' % rgb
def hls2hex(h, l, s):
return rgb2hex( tuple([int(x*255) for x in colorsys.hls_to_rgb(h, l, s)]))
lightness = 1 - (value * BASE_LIGHTNESS) / max_value
return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)
heatmap_data = {}
max_value, min_value = None, None
for line in open(args.heatmap):
if line.startswith('#COLNAMES'):
pass
elif line.startswith('#') or not line.strip():
pass
else:
fields = line.split('\t')
name = fields[0].strip()
values = [float(x) if x else None for x in fields[1:]]
maxv = max(values)
minv = min(values)
if max_value is None or maxv > max_value:
max_value = maxv
if min_value is None or minv < min_value:
min_value = minv
heatmap_data[name] = values
heatmap_center_value = 0
heatmap_color_center = "white"
heatmap_color_up = 0.3
heatmap_color_down = 0.7
heatmap_color_missing = "black"
heatmap_max_value = abs(heatmap_center_value - max_value)
heatmap_min_value = abs(heatmap_center_value - min_value)
if heatmap_center_value <= min_value:
heatmap_max_value = heatmap_min_value + heatmap_max_value
else:
heatmap_max_value = max(heatmap_min_value, heatmap_max_value)
# scale the tree
if not args.height:
args.height = None
if not args.width:
args.width = None
f2color = {}
f2last_seed = {}
for node in t.traverse():
node.img_style['size'] = 0
if len(node.children) == 1:
node.img_style['size'] = 2
node.img_style['shape'] = "square"
node.img_style['fgcolor'] = "steelblue"
ftype_pos = defaultdict(int)
for findex, f in enumerate(FACES):
if (f['nodetype'] == 'any' or
(f['nodetype'] == 'leaf' and node.is_leaf()) or
(f['nodetype'] == 'internal' and not node.is_leaf())):
# if node passes face filters
if node_matcher(node, f["filters"]):
if f["value"].startswith("@"):
fvalue = getattr(node, f["value"][1:], None)
else:
fvalue = f["value"]
# if node's attribute has content, generate face
if fvalue is not None:
fsize = f["size"]
fbgcolor = f["bgcolor"]
fcolor = f['color']
if fcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fcolor = f2color.setdefault(color_bin, random_color(h=seed))
if fbgcolor:
# Parse color options
auto_m = re.search("auto\(([^)]*)\)", fbgcolor)
if auto_m:
target_attr = auto_m.groups()[0].strip()
if not target_attr :
color_keyattr = f["value"]
else:
color_keyattr = target_attr
color_keyattr = color_keyattr.lstrip('@')
color_bin = getattr(node, color_keyattr, None)
last_seed = f2last_seed.setdefault(color_keyattr, random.random())
seed = last_seed + 0.10 + random.uniform(0.1, 0.2)
f2last_seed[color_keyattr] = seed
fbgcolor = f2color.setdefault(color_bin, random_color(h=seed))
if f["ftype"] == "text":
if f.get("format", None):
fvalue = f["format"] % fvalue
F = TextFace(fvalue,
fsize = fsize,
fgcolor = fcolor or "black",
fstyle = f.get('fstyle', None))
elif f["ftype"] == "fullseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="seq",
seqtail_format="seq",
height=fsize)
elif f["ftype"] == "compactseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="compactseq",
seqtail_format="compactseq",
height=fsize)
elif f["ftype"] == "blockseq":
F = faces.SeqMotifFace(seq=fvalue, seq_format="blockseq",
seqtail_format="blockseq",
height=fsize,
fgcolor=fcolor or "slategrey",
bgcolor=fbgcolor or "slategrey",
scale_factor = 1.0)
fbgcolor = None
elif f["ftype"] == "bubble":
try:
v = float(fvalue)
except ValueError:
rad = fsize
else:
rad = fsize * v
F = faces.CircleFace(radius=rad, style="sphere",
color=fcolor or "steelblue")
elif f["ftype"] == "heatmap":
if not f['column']:
col = ftype_pos[f["pos"]]
else:
col = f["column"]
for i, value in enumerate(heatmap_data.get(node.name, [])):
ftype_pos[f["pos"]] += 1
if value is None:
color = heatmap_color_missing
elif value > heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_up)
elif value < heatmap_center_value:
color = gradient_color(abs(heatmap_center_value - value), heatmap_max_value, hue=heatmap_color_down)
else:
color = heatmap_color_center
node.add_face(RectFace(20, 20, color, color), position="aligned", column=col + i)
# Add header
# for i, name in enumerate(header):
# nameF = TextFace(name, fsize=7)
# nameF.rotation = -90
# tree_style.aligned_header.add_face(nameF, column=i)
F = None
elif f["ftype"] == "profile":
# internal profiles?
F = None
elif f["ftype"] == "barchart":
F = None
elif f["ftype"] == "piechart":
F = None
# Add the Face
if F:
F.opacity = f['opacity'] or 1.0
# Set face general attributes
if fbgcolor:
F.background.color = fbgcolor
if not f['column']:
col = ftype_pos[f["pos"]]
ftype_pos[f["pos"]] += 1
else:
col = f["column"]
node.add_face(F, column=col, position=f["pos"])
if args.image:
t.render("t%d.%s" %(tindex, args.image),
tree_style=ts, w=args.width, h=args.height, units=args.size_units)
else:
t.show(None, tree_style=ts)
else:
#We're at the root node
new_node.dist = 0
cur_node_id = str(current_bud_row.OrgID)
for idx, new_row in saved_pop_hosts[saved_pop_hosts.ParentID.eq(cur_node_id)].iterrows():
build_tree_recursive(new_row, new_node)
return new_node
root_node_row = saved_pop_hosts[saved_pop_hosts.ParentID == "(none)"].squeeze()
print("Building Tree")
build_tree_recursive(root_node_row, host_phylo)
print("Drawing Tree")
#Some drawing code
ts = TreeStyle()
ts.show_leaf_name = True
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
host_phylo.render("tree.png", tree_style=ts)
print("Saving Tree")
#Write the Newick Format Tree
host_phylo.write(format=1, outfile="avida_tree.nw")
nstyle['bgcolor'] = cp[0]
elif abr == 'pbi':
nstyle['bgcolor'] = cp[1]
elif abr == 'pte':
nstyle['bgcolor'] = cp[2]
elif abr == 'ppe':
nstyle['bgcolor'] = cp[3]
elif abr == 'pse':
nstyle['bgcolor'] = cp[4]
elif abr == 'poc':
nstyle['bgcolor'] = cp[5]
elif abr == 'ptr':
nstyle['bgcolor'] = cp[6]
elif abr == 'pso':
nstyle['bgcolor'] = cp[7]
elif abr == 'pca':
nstyle['bgcolor'] = cp[8]
elif abr == 'tth':
nstyle['bgcolor'] = cp[9]
else:
nstyle['bgcolor'] = "#000000"
node.set_style(nstyle)
ts = TreeStyle()
#ts.show_leaf_name = False
ts.mode = 'c'
ts.title.add_face(TextFace(title, fsize=20), column=0)
#t.show(tree_style = ts)
t.render(outputfile, tree_style = ts)
@author: diyadas
This script plots trees of our wikipedia data.
"""
from ete3 import Tree, TreeStyle, NodeStyle
with open('/Users/diyadas/cdips/Topic-Ontology/SimpleWikiTree_u.txt','r') as f:
treestr = f.readlines()[0]
t = Tree( treestr.rstrip(),format=8)
circular_style = TreeStyle()
circular_style.mode = "c" # draw tree in circular mode
circular_style.scale = 120
circular_style.show_leaf_name = True
circular_style.show_branch_length = True
circular_style.show_branch_support = True
t.render("mytree.png", tree_style=circular_style)
nstyle = NodeStyle()
nstyle["hz_line_width"] = 3
nstyle["vt_line_width"] = 3
# Applies the same static style to all nodes in the tree. Note that,
# if "nstyle" is modified, changes will affect to all nodes
for n in t.traverse():
n.set_style(nstyle)
#root = Tree( "((a,b),c);" )
[rows, columns] = treeStruct.shape
root = Tree()
node_cur = root
'''#######################
Tree Style Begin
'''
ts = TreeStyle()
ts.title.add_face(TextFace("Tree example", fsize=8), column=0)
ts.scale = 50
ts.mode = 'r'
# left or right
ts.orientation = 1
ts.rotation = 270
ts.show_leaf_name = False
ts.show_branch_length = True
#ts.show_branch_length = True
'''
Tree Style End
#######################'''
application.CONFIG["DISPLAY"] = ":0" # This is the most common
# configuration
# We extend the minimum WebTreeApplication with our own WSGI
# application
application.set_external_app_handler(example_app)
# Lets now apply our custom tree loader function to the main
# application
application.set_tree_loader(my_tree_loader)
# And our layout as the default one to render trees
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn.append(main_layout)
ts.mode = "r"
ts.branch_vertical_margin = 5
#ts.scale = 20
application.set_tree_style(ts)
#application.set_default_layout_fn(main_layout)
application.set_tree_size(None, None)
# I want to make up how tree image in shown using a custrom tree
# renderer that adds much more HTML code
application.set_external_tree_renderer(tree_renderer)
# ==============================================================================
# ADD CUSTOM ACTIONS TO THE APPLICATION
#
# The function "register_action" allows to attach functionality to
# nodes in the image. All registered accions will be shown in the
def main(args):
if args.alignment:
t = PhyloTree(args.tree, alignment=args.alignment, alg_format='fasta')
else:
t = PhyloTree(args.tree)
if args.highlight_new:
runs = read_runs(args.highlight_new)
t.set_outgroup('EM_079422')
t.ladderize()
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_support = False
ts.layout_fn = layout
thick_hz_line = NodeStyle()
thick_hz_line["hz_line_width"] = 8
t.set_style(thick_hz_line)
#t.children[0].set_style(thick_hz_line)
#t.children[1].set_style(thick_hz_line)
thick_vt_line = NodeStyle()
thick_vt_line["vt_line_width"] = 4
t.set_style(thick_vt_line)
# header
if not args.hide_annotations:
ts.aligned_header.add_face(MyTextFace('Sample identifier', fstyle='Bold', fsize=8, tight_text=False), column = 1)
ts.aligned_header.add_face(MyTextFace('Prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 2)
ts.aligned_header.add_face(MyTextFace('Sous-prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 3)
ts.aligned_header.add_face(MyTextFace('Village', fstyle='Bold', fsize=8, tight_text=False), column = 4)
ts.aligned_header.add_face(MyTextFace('Sample received', fstyle='Bold', fsize=8, tight_text=False), column = 5)
if args.positions:
positions = read_positions(args.positions)
alg_header = RulerFace(positions,
col_width=11,
height=0, # set to 0 if dont want to use values
kind="stick",
hlines = [0],
hlines_col = ["white"], # trick to hide hz line
)
ts.aligned_header.add_face(alg_header, 6)
#legend
if args.legend:
legend = {}
for s in samples.values():
legend[s['prefec']] = s['prefec__colour']
for p in sorted(legend.keys()):
ts.legend.add_face(CircleFace(4, legend[p]), column=0)
ts.legend.add_face(MyTextFace(p, fsize=6, tight_text=False), column=1)
ts.legend_position=1
if args.circular:
ts.mode = "c"
ts.arc_start = -180 # 0 degrees = 3 o'clock
ts.arc_span = 180
# t.show(tree_style=ts)
t.render(args.output, tree_style=ts, w=1024)
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
faces.add_face_to_node(name, node, 0, aligned=True)
fake = faces.TextFace(" ")
fake.background.color = "white"
faces.add_face_to_node(fake, node, 1, aligned=True) # fake
else:
if not args.no_internal_names and node.get_distance(tNCBI, topology_only=True) < 3:
name = faces.TextFace(node.sci_name, fsize=12, fstyle='italic')
faces.add_face_to_node(name, node, 0, position='branch-top')
S = TreeStyle()
#S.allow_face_overlap = True
S.show_leaf_name = False
#S.scale = 200
#S.draw_aligned_faces_as_table = True
#S.aligned_table_style = 0
#S.min_leaf_separation = 1
if args.mode == 'r':
S.mode = 'r'
elif args.mode == 'c':
S.mode = 'c'
if args.save:
tNCBI.render(file_name=args.save, layout=layout, tree_style=S)
else:
print "showing"
tNCBI.show(layout=layout, tree_style=S)
