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 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("( π²,( π₯,(( π·, ( π΄, ( π, ( π, ( π½, ( π, πΎ )))))),(( π, ((( π₯, βοΈ), ((( πΉ, π ), (( π, π ), ( π, (πΈ, π) ))), ( π°, ( π, ( π, ( π₯, π)))))), (( πΊ, π₯¦ ), (( π, π ), ( π, π₯))))),( π΅, ( π₯, (( π , ( πΆοΈ, (π, ( π₯, π
)))), ( π₯,( π₯¬, ( π», πΌ)))))))));")
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 custom_treestyle():
ts = TreeStyle()
ts.layout_fn = custom_layout
ts.show_leaf_name = False
ts.branch_vertical_margin = 0
ts.min_leaf_separation = 0
return ts
def generate_type_tree_figure(output_file):
""" Generate type_tree.png image.
It needs ETE dependencies installed
cf http://etetoolkit.org/new_download/ or use anaconda
:param output_file: str
"""
try:
from ete3 import faces, TextFace, TreeStyle
except ImportError as e:
logger.warning(
'ImportError : %s Generation of type_tree figure need ETE dependencies to '
'be installed Use from anaconda, or look at installation procedure on '
'http://etetoolkit.org/new_download/', e)
return
# Define custom tree style
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.orientation = 1
ts.branch_vertical_margin = 20
def my_layout(node):
F = TextFace(node.name, fsize=16, ftype='Courier', bold=True)
faces.add_face_to_node(F, node, column=10, position="branch-right")
ts.layout_fn = my_layout
TYPES_STRING_TREE.render(output_file, tree_style=ts)
def createImg(filename, thres=0, samples=1):
count = parseLineage(filename)
suffix, matrix, taxo = getSuffixandMatrixandNewick(count,thres,samples)
newick = convert(taxo,suffix)
newick += ';'
t = Tree(newick, format=1)
ct = ClusterTree(t.write(), text_array=matrix)
addColors(ct)
# nodes are linked to the array table
array = ct.arraytable
# Calculates some stats on the matrix. Needed to establish the color gradients.
matrix_dist = [i for r in xrange(len(array.matrix))for i in array.matrix[r] if np.isfinite(i)]
matrix_max = np.max(matrix_dist)
matrix_min = np.min(matrix_dist)
matrix_avg = (matrix_max+matrix_min)/2
# Creates a profile face that will represent node's profile as a heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 14, "heatmap",colorscheme=3)
# Creates my own layout function that uses previous faces
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"]=2
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
# ct.show(tree_style=ts)
filedir = '/'.join(filename.split('/')[:-1])
# t.write(format=9, outfile="output/newick/"+param+".nw")
ct.render(filedir+'/phylo.png',tree_style=ts)
def get_example_tree():
# Random tree
t = Tree()
t.populate(20, random_branches=True)
# Some random features in all nodes
for n in t.traverse():
n.add_features(weight=random.randint(0, 50))
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
ts.mode = "c"
# We will add node names manually
ts.show_leaf_name = False
# Show branch data
ts.show_branch_length = True
ts.show_branch_support = True
return t, ts
def 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 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():
# 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 ete_draw(self, fname=None):
""" Draws the tree and saves it to a file. If `fname` is None,
show the tree instead of saving it.
Args:
fname: filename to save to (default=None)
"""
if Cfg.USE_ETE3:
def layout(node):
faces.add_face_to_node(AttrFace("name"),
node,
column=0,
position="branch-right")
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = layout
ts.rotation = 90
tree = EteTree(self.ete_str(), format=8)
if fname:
tree.render(fname, tree_style=ts)
else:
tree.show(tree_style=ts)
else:
# TODO maybe throw an error?
pass
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 draw_raw_tree(filename: str) -> None:
"""Draws a raw tree from ete3 representation
stored in a file
Parameters
----------
filename : str
a name of the file
Returns
-------
None
"""
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = layout_raw
ts.rotation = 90
ts.branch_vertical_margin = 10
ts.show_scale = False
ts.scale = 50
ts.title.add_face(TextFace(" ", fsize=20), column=0)
ete3_desc = read_ete3_from_file(filename)
tree = Tree(ete3_desc, format=1)
# tree.show(tree_style=ts)
return tree.render("%%inline",tree_style=ts)
def ete_draw(self, fname=None):
""" Draws the tree and saves it to a file. If `fname` is None,
show the tree instead of saving it.
Args:
fname: filename to save to (default=None)
"""
if Cfg.USE_ETE3:
def layout(node):
faces.add_face_to_node(AttrFace("name"), node, column=0,
position="branch-right")
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = layout
ts.rotation = 90
tree = EteTree(self.ete_str(), format=8)
if fname:
tree.render(fname, tree_style=ts)
else:
tree.show(tree_style=ts)
else:
# TODO maybe throw an error?
pass
def make_tree(t):
ts = TreeStyle()
## make the tree in to a cladogram
most_distant_leaf, tree_length = t.get_farthest_leaf()
current_dist = 0
for postorder, node in t.iter_prepostorder():
if postorder:
current_dist -= node.dist
else:
if node.is_leaf():
node.dist += tree_length - (current_dist + node.dist)
elif node.up: # node is internal
current_dist += node.dist
## Rotate and color the lables
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")
## Format the tree image
nstyle = NodeStyle()
nstyle["hz_line_type"] = 0
nstyle["vt_line_color"] = "#ffffff"
nstyle["hz_line_color"] = "#ffffff"
nstyle["vt_line_width"] = 4
nstyle["hz_line_width"] = 4
nstyle["size"] = 0
for n in t.traverse():
n.set_style(nstyle)
## Set background
t.img_style["bgcolor"] = "#2e3440"
## Tree 'shape'
ts.min_leaf_separation = 20
ts.show_leaf_name = False
ts.layout_fn = rotation_layout
ts.rotation = -90
ts.show_scale = False
#t.show(tree_style=ts)
t.render(f"{t.name}.svg", tree_style=ts, dpi=900)
def show_and_render_tree(tree, output_file_name, mut_order):
# The following makes it show internal nodes
def my_layout(node):
if hasattr(node, 'has_face'):
return
if node.is_leaf():
# If terminal node, draws its name
name_face = AttrFace("name", fsize=12)
node.add_face(name_face, column=0, position="branch-right")
else:
# If internal node, draws label with smaller font size
if node.name == 'root':
label = 'root'
else:
label = str(mut_order[int(node.name)])
name_face = TextFace(label, fsize=10)
node.add_face(name_face, column=0, position="branch-top")
node.add_feature('has_face', True)
# Adds the name face to the image at the preferred position
#faces.add_face_to_node(name_face, node, column=0, position="branch-top")
ts = TreeStyle()
# Do not add leaf names automatically
ts.show_leaf_name = False
# Use my custom layout
ts.layout_fn = my_layout
tree.show(tree_style=ts)
tree.render(output_file_name, tree_style=ts, dpi=180)
def get_example_tree():
# Random tree
t = Tree()
t = Tree(
"(((yessefk),(ad, tuΙ£al),((teqbaylit),(d,(tutlayt,tunαΉ£ibt)))),(((win,yebΙ£an), (taqbaylit)),(((ad,yissin, (tira,-s))))),(((win,yebΙ£an), (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 compute_minimum_spanning_tree(file_name, artists, distance_matrix, authors,
styles, list_period_color):
dst_list = []
max = len(distance_matrix[-1])
for line in distance_matrix:
remain = max - len(line)
dst_list.append(line + [0.0] * remain)
G = np.array(dst_list)
Tcsr = minimum_spanning_tree(G)
G = nx.Graph(Tcsr)
elst = bfs_edge_lst(G, 1)
tree = tree_from_edge_lst(elst)
newick_minimum_spanning_tree = tree_to_newick(tree) + ';'
t = Tree(newick_minimum_spanning_tree)
vl = []
for node in t.traverse("postorder"):
if node.is_leaf():
name = artists[int(node.name)]
node.name = name
else:
name = artists[int(node.support)]
node.name = name
vl.append(node.name)
ts = TreeStyle()
ts, t = set_default_TreeStyle(t)
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")
ts.layout_fn = my_layout
list_of_nodes = {}
for author in authors:
for node in t.traverse("postorder"):
if (node.name == author):
new_dic = get_sister_common_styles(node, artists, styles)
list_of_nodes.update(new_dic)
prevalent_dict = most_prevalent(list_of_nodes)
for author in authors:
for node in t.traverse("postorder"):
if (node.name == author):
attribute_legend(node, authors, styles)
add_painting(node, im, basename)
savename_period = "../plots/" + file_name + "Kruskal_minimum_spanning_tree.pdf"
t.render(savename_period, tree_style=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 custom_treestyle():
#Add treestyle
ts = TreeStyle()
#use custom layout fuction
ts.layout_fn = custom_layout
#don't show leaf names (leaf names can be customized in custom layout)
ts.show_leaf_name = False
return 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_tree_style(self):
ts = TreeStyle()
ts.layout_fn = self.custom_layout
ts.show_leaf_name = False
ts.draw_guiding_lines = True
#ts.guiding_lines_type = 1
self._treestyle = ts
return ts
def export_tree(tree, filename, insignif_color, signif_color, i_group, width):
'''
exports the given tree to the given filename
'''
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_scale = False
ts.layout_fn = generate_layout(insignif_color, signif_color, i_group)
tree.render(filename, w=width, tree_style=ts)
def get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_leaf_name = True
ts.min_leaf_separation = 15
t.populate(100)
return t, ts
def get_example_tree():
t = Tree()
t.populate(10)
ts = TreeStyle()
ts.rotation = 45
ts.show_leaf_name = False
ts.layout_fn = rotation_layout
return t, ts
def get_example_tree():
t = Tree()
t.populate(8, reuse_names=False)
ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
return t, ts
def 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 get_example_tree():
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_leaf_name = True
ts.min_leaf_separation = 15
t.populate(100)
return t, ts
def get_example_tree():
t = Tree()
t.populate(8, reuse_names=False)
ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
return t, ts
def plot_tree(tree, leafname2data = None , show_support = False, figname = None, outfname_tree = None): def layout(node): nst_internal = NodeStyle() nst_internal['size'] = 1 nst_internal['fgcolor'] = 'black' nst_internal["vt_line_color"] = "black" nst_internal["hz_line_color"] = "black" nst_internal["vt_line_width"] = 1 nst_internal["hz_line_width"] = 1 nst_internal["vt_line_type"] = 0 #0 solid, 1 dashed, 2 dotted nst_internal["hz_line_type"] = 0 node.set_style(nst_internal) if leafname2data != None and node.is_leaf(): if not node.name[0] == '_': print(node.name) nst = NodeStyle() node_data = leafname2data[node.name] node_name = node.name node_shape = None node_color = None if len(node_data) >= 3: node_name = node_data[0] node_shape = node_data[1] node_color = '#'+node_data[2].lower() else: node_shape = node_data[0] node_color = '#'+node_data[1].lower() nst['size'] = 15 nst['shape'] = node_shape nst['fgcolor'] = node_color node.set_style(nst) #node.add_face(TextFace(node_name, ftype='Verdana', fsize=12), column = 0, position = "aligned") ts = TreeStyle() ts.layout_fn = layout ts.show_leaf_name = False if show_support: ts.show_branch_support = True ts.branch_vertical_margin = 10 if outfname_tree != None: tree.write(outfile = outfname_tree) if figname != None: tree.render(figname, layout=layout, w=None, h=None, tree_style=ts, units='px', dpi=300) else: tree.show(tree_style=ts)
def get_example_tree():
with open("avian_tree", "r") as infile:
data = infile.read()
t = Tree(data)
ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
return t, ts
def get_tree_style():
ts = TreeStyle()
ts.show_leaf_name = False # True
ts.layout_fn = layout
ts.rotation = 90
ts.branch_vertical_margin = 10
ts.show_scale = False
# ts.mode = "c"
ts.scale = 50
ts.title.add_face(TextFace(" ", fsize=20), column=0)
# for n in t.traverse():
# nstyle = NodeStyle()
# nstyle["fgcolor"] = "red"
# nstyle["size"] = 15
# n.set_style(nstyle)
# ts.show_leaf_name = True
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, NO_SUPPORT_COLOR, NO_SUPPORT_COLOR),
column=0)
ts.legend.add_face(TextFace(" Topic with no support (u(t)=0)"), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "#90ee90", "#90ee90"), column=0)
ts.legend.add_face(TextFace(" Topic with minor support 0<u(t)<=0.4"),
column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "green", "green"), column=0)
ts.legend.add_face(
TextFace(u" Topic with medium support 0.4<u(t)<=0.6 "), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(20, 20, "#004000", "#004000"), column=0)
ts.legend.add_face(TextFace(" Topic with high support u(t)>0.6"),
column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(CircleFace(10, "red"), column=0)
ts.legend.add_face(TextFace(" Gap"), column=1)
ts.legend.add_face(TextFace(" "), column=0)
ts.legend.add_face(TextFace(" "), column=1)
ts.legend.add_face(RectFace(40, 40, "#004000", "#004000"),
column=0) # green
# ts.legend.add_face(CircleFace(15, "green"), column=1)
ts.legend.add_face(TextFace(" Head subject or offshoot"), column=1)
ts.legend_position = 4
# ts.title.add_face(TextFace(" ", fsize=20), column=0)
return ts
def set_tree_style_extended():
ts = TreeStyle()
# for i in range(16):
# ts.legend.add_face(CircleFace(10, color_dictionary["N{0}".format(i)]), column=0)
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
ts.layout_fn = my_layout_extended
return ts
def show(self):
"""
Allows user to quickly view LinkTree
"""
style = TreeStyle()
style.show_leaf_name = False
def my_layout(node):
node_style = TextFace(node.name, tight_text=True)
add_face_to_node(node_style, node, column=0, position='branch-bottom')
style.layout_fn = my_layout
self._tree.show(tree_style=style)
def get_example_tree():
t = Tree()
t.populate(8)
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)
#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0
style1["vt_line_color"] = "#ff0000"
style1["hz_line_color"] = "#ff0000"
style1["vt_line_width"] = 2
style1["hz_line_width"] = 2
style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
style1["hz_line_type"] = 2
t.children[0].img_style = style1
t.children[1].img_style = style1
# Set dashed blue lines in all leaves
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
style2["vt_line_color"] = "#0000aa"
style2["hz_line_color"] = "#0000aa"
style2["vt_line_width"] = 2
style2["hz_line_width"] = 2
style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
style2["hz_line_type"] = 1
for l in t.iter_leaves():
l.img_style = style2
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
return t, ts
def get_example_tree():
t = Tree()
t.populate(8)
# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)
# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)
#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0
style1["vt_line_color"] = "#ff0000"
style1["hz_line_color"] = "#ff0000"
style1["vt_line_width"] = 2
style1["hz_line_width"] = 2
style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
style1["hz_line_type"] = 2
t.children[0].img_style = style1
t.children[1].img_style = style1
# Set dashed blue lines in all leaves
style2 = NodeStyle()
style2["fgcolor"] = "#000000"
style2["shape"] = "circle"
style2["vt_line_color"] = "#0000aa"
style2["hz_line_color"] = "#0000aa"
style2["vt_line_width"] = 2
style2["hz_line_width"] = 2
style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
style2["hz_line_type"] = 1
for l in t.iter_leaves():
l.img_style = style2
ts = TreeStyle()
ts.layout_fn = layout
ts.show_leaf_name = False
return t, ts
def _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 run_action_change_style(self, tree, a_data):
#print "action change style called.."
if tree.tree_style == self._treestyle:
ts2 = TreeStyle()
ts2.layout_fn = self.custom_layout
ts2.show_leaf_name = False
ts2.draw_guiding_lines = True
ts2.guiding_lines_type = 0 #solid line
ts2.guiding_lines_color = a_data
tree.tree_style = ts2
self._treestyle = ts2
else:
tree.tree_style = self._treestyle
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 draw_ete3_tree(organism, snplist, tree_file_name, config, c):
'''Draws a phylogenetic tree using ETE3
Keyword arguments:
organism -- the organism of which to make a tree
snplist -- a list of the SNP names, positions and state
file_name -- the name of the out-file _tree.pdf will be added
'''
newick = tree_to_newick(organism, config, c)
tree = Tree(newick, format=1)
tree_depth = int(tree.get_distance(tree.get_farthest_leaf()[0]))
for n in tree.traverse():
# Nodes are set to red colour
nstyle = NodeStyle()
nstyle["fgcolor"] = "#BE0508"
nstyle["size"] = 10
nstyle["vt_line_color"] = "#000000"
nstyle["hz_line_color"] = "#000000"
nstyle["vt_line_type"] = 0
nstyle["hz_line_type"] = 0
nstyle["vt_line_width"] = 2
nstyle["hz_line_width"] = 2
## ['B.3', 'T', 'C', 'A']
for snp in snplist.keys():
if n.name == snp and snplist[snp] == 0:
# If the SNP is missing due to a gap, make it grey
nstyle["fgcolor"] = "#DDDDDD"
nstyle["size"] = 10
nstyle["vt_line_color"] = "#DDDDDD"
nstyle["hz_line_color"] = "#DDDDDD"
nstyle["vt_line_type"] = 1
nstyle["hz_line_type"] = 1
elif n.name == snp and snplist[snp] == 1:
nstyle["fgcolor"] = "#99FF66"
nstyle["size"] = 15
nstyle["vt_line_color"] = "#000000"
nstyle["hz_line_color"] = "#000000"
nstyle["vt_line_type"] = 0
nstyle["hz_line_type"] = 0
n.set_style(nstyle)
ts = TreeStyle()
ts.show_leaf_name = False # Do not print(leaf names, they are added in layout)
ts.show_scale = False # Do not show the scale
ts.layout_fn = self.CanSNPer_tree_layout # Use the custom layout
ts.optimal_scale_level = 'full' # Fully expand the branches of the tree
if config["dev"]:
print("#[DEV] Tree file: %s" % tree_file_name)
tree.render(tree_file_name, tree_style=ts, width=tree_depth * 500)
def tree2img(newick_tree, save_path):
t = Tree(newick_tree, format=1)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_length = False
ts.show_branch_support = False
def my_layout(node):
F = TextFace(node.name, tight_text=True)
add_face_to_node(F, node, column=0, position="branch-right")
ts.layout_fn = my_layout
ts.branch_vertical_margin = 10
ts.rotation = 90
t.render(save_path+'png', tree_style=ts)
t.render(save_path+'svg', 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 get_example_tree():
# Create a random tree and add to each leaf a random set of motifs
# from the original set
t = Tree()
t.populate(10)
# for l in t.iter_leaves():
# seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))
# seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
# seqtail_format="compactseq", scale_factor=1)
# seqFace.margin_bottom = 4
# f = l.add_face(seqFace, 0, "aligned")
ts = TreeStyle()
ts.layout_fn = layout
return t, ts
def draw_tree(tree_string):
t = Tree(tree_string, format=8)
def mylayout(node):
#if node.name != 'L':
file = 'tmp/%s.png' % node.name
new_face = faces.ImgFace(file)
new_face.rotable = True
new_face.rotation = -90
#new_face.margin_top = 50
new_face.margin_left = 15
faces.add_face_to_node(new_face, node, column=0 , position='branch-top')
ts = TreeStyle()
ts.rotation = 90
ts.layout_fn = mylayout
t.show(tree_style = ts)
plt.clf()
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 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)
Rangifer_tarandus,http://media.eol.org/content/2014/05/02/09/88803_98_68.jpg,109.09,herbivore
Cervus_elaphus,http://media.eol.org/content/2013/02/22/16/31998_98_68.jpg,240.87,herbivore
Bos_taurus,http://media.eol.org/content/2014/09/29/06/46535_98_68.jpg,618.64,herbivore
Ovis_orientalis,http://media.eol.org/content/2015/01/04/05/30107_98_68.jpg,39.1,herbivore
Suricata_suricatta,http://media.eol.org/content/2012/06/19/04/84840_98_68.jpg,0.73,carnivore
Mephitis_mephitis,http://media.eol.org/content/2012/08/30/16/23686_98_68.jpg,2.4,omnivore"""
tip2info = {}
for line in tip_info_csv.split('\n'):
if line:
name, url, mass, habit = map(str.strip, line.split(','))
tip2info[name] = [url, mass, habit]
# Server configuration
ts = TreeStyle()
ts.layout_fn = custom_layout
ts.show_leaf_name = False
ts2 = TreeStyle()
actions = NodeActions()
actions.add_action('Root here', show_action_root, run_action_root, None)
actions.add_action('Highlight', show_action_highlight, run_action_highlight, None)
actions.add_action('Change style', show_action_change_style, run_action_change_style, None)
actions.add_action('EOL link', show_eol_link, None, eol_link)
actions.add_action('Change color', show_action_linecolor, None, change_linecolor)
start_server(node_actions=actions, tree_style=ts)
if "highlighted" in node.features:
node.img_style["bgcolor"] = "LightCyan"
if "improve" in node.features:
color = "orange" if float(node.improve) < 0 else "green"
if float(node.improve) == 0:
color = "blue"
support_face = faces.CircleFace(200, color)
faces.add_face_to_node(support_face, node, 0, position="float-behind")
try:
from ete3 import TreeStyle, NodeStyle, faces
from ete3.treeview import random_color
NPR_TREE_STYLE = TreeStyle()
NPR_TREE_STYLE.layout_fn = npr_layout
NPR_TREE_STYLE.show_leaf_name = False
except ImportError:
TreeStyle, NodeStyle, faces, random_color = [None]*4
NPR_TREE_STYLE = None
# CONVERT shell colors to the same curses palette
COLORS = {
"wr": '\033[1;37;41m', # white on red
"wo": '\033[1;37;43m', # white on orange
"wm": '\033[1;37;45m', # white on magenta
"wb": '\033[1;37;46m', # white on blue
"bw": '\033[1;37;40m', # black on white
"lblue": '\033[1;34m', # light blue
#
# 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)
ts.layout_fn = my_layout
t.render('treefig.png', tree_style=ts)
# for key in prune_count.keys():
# # node_weight = ln(prune_count[key])
# # node_weight = ln(n_children)
# # print(node_weight,n_children)
# # node = lookup[key]
# node.add_features(weight=random.randint(50))
for n in t.traverse():
n.add_face(TextFace(n.name, fsize = 16), column=0, position="branch-bottom")
# n.add_features(weight=random.randint(0,20))
t.prune(prune_list)
# Create an empty TreeStyle
ts = TreeStyle()
# Set our custom layout function
ts.layout_fn = layout
# Draw a tree
# ts.mode = "c" # this makes it circular
# False need to add node names manually
ts.show_leaf_name = False
ts.scale = 120
# Show branch data
ts.show_branch_length = False
ts.show_branch_support = True
# print (t.get_ascii(show_internal=True))
t.show(tree_style=ts)
concord_text = faces.TextFace(str(int(concord_dict[mynode.name]))+' ',fsize=20)
conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name]))+' ',fsize=20)
faces.add_face_to_node(concord_text,mynode,0,position = "branch-top")
faces.add_face_to_node(conflict_text,mynode,0,position="branch-bottom")
else:
F = faces.TextFace(mynode.name,fsize=20)
faces.add_face_to_node(F,mynode,0,position="aligned")
#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False
ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
n.set_style(nstyle)
n.img_style["vt_line_width"] = 0
ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
plot_tree.ladderize(direction=1)
my_svg = plot_tree.render(args.svg_name,tree_style=ts,w=595,dpi=300)
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
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>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
tree.show(tree_style=ts)
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)
# 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)
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
t.children[0].show(tree_style=ts)
