def do_layout(self, tree):
"""
Interleave the processes of breaking the tree and daylight equalization.
@param tree: something like a SpatialTree
"""
# reroot to a node with more than two neighbors
if get_neighbor_count(tree.root) < 3:
suitable_roots = [
x for x in tree.preorder() if get_neighbor_count(x) > 2
]
if suitable_roots:
tree.reroot(suitable_roots[0])
# create the initial layout
EqualArcLayout.do_layout(tree)
# determine the maximum allowed branch length
total_branch_length = tree.get_total_length()
max_branch_length = total_branch_length / float(self.min_segment_count)
# any branch longer than the max branch length will be broken in half
iteration = 0
while True:
print 'progressive iteration', iteration + 1
# write the extension tree
dtree = day.Day()
_build_dtree(dtree, tree.root, 0)
# equalize the layout
for node in tree.breadth_first():
if get_neighbor_count(node) > 1:
dtree.select_node(node.dtree_id)
dtree.reroot()
try:
dtree.equalize()
except RuntimeError as e:
raise LayoutError(e)
# read the extension tree
for node in tree.preorder():
dtree.select_node(node.dtree_id)
x = dtree.get_x()
y = dtree.get_y()
node.location = (x, y)
# break the branches
old_nodes = list(tree.preorder())
for node in old_nodes:
if node is tree.root:
if node.blen is not None:
raise HandlingError(
'the root node should not have a branch length')
elif node.blen is None:
raise HandlingError(
'each non-root node should have a branch length')
elif node.blen > max_branch_length:
# create a new node and set its attributes
new = self.node_factory()
new.name = node.name
# insert the new node
tree.insert_node(new, node.parent, node, .5)
# if no node was added then break out of the loop
if len(old_nodes) == len(list(tree.preorder())):
break
else:
iteration += 1
def main():
import EqualArcLayout
import Newick
import SpatialTree
# make a spatial tree
tree = Newick.parse(Newick.daylight_example_tree, SpatialTree.SpatialTree)
EqualArcLayout.do_layout(tree)
max_size = (640, 480)
image_formats = ('png', 'pdf', 'ps', 'svg')
for image_format in image_formats:
# get the image string
image_string = get_tree_image(tree, max_size, image_format)
# write the image file
image_filename = 'test.%s' % image_format
with open(image_filename, 'wb') as fout:
fout.write(image_string)
print 'created', image_filename
# write an html file
html_filename = 'test.html'
with open(html_filename, 'w') as fout:
print >> fout, '<html><body>'
for image_format in image_formats:
image_filename = 'test.%s' % image_format
print >> fout, '<a href="%s">%s</a><br/>' % (image_filename,
image_filename)
print >> fout, '</body></html>'
print 'created', html_filename
def do_layout(self, tree):
"""
@param tree: something like a SpatialTree
"""
# create the initial layout
EqualArcLayout.do_layout(tree)
# use sax-like events to create a parallel tree in the C extension
dtree = day.Day()
count = _build_dtree(dtree, tree.root, 0)
# repeatedly reroot and equalize
for iteration in range(self.iteration_count):
for node in tree.breadth_first():
neighbor_count = len(node.children)
if node.parent:
neighbor_count += 1
if neighbor_count > 2:
dtree.select_node(node.dtree_id)
dtree.reroot()
try:
dtree.equalize()
except RuntimeError as e:
raise LayoutError(e)
# extract the x and y coordinates from the parallel tree
for node in tree.preorder():
dtree.select_node(node.dtree_id)
x = dtree.get_x()
y = dtree.get_y()
node.location = (x, y)
# take off the silly dtree_id members
for node in tree.preorder():
del node.dtree_id
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
tree.assert_valid()
if tree.has_negative_branch_lengths():
msg = 'drawing a tree with negative branch lengths is not implemented'
raise HandlingError(msg)
tree.add_branch_lengths()
# do the layout
if fs.daylight:
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
elif fs.curved:
try:
layout = FastDaylightLayout.CurvedBranchLayout()
layout.set_min_segment_count(400)
layout.do_layout(tree)
except RuntimeError as e:
pass
elif fs.arc:
EqualArcLayout.do_layout(tree)
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawTreeImage.get_tree_image(tree, (640, 480), ext)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
tree.assert_valid()
if tree.has_negative_branch_lengths():
msg = 'drawing a tree with negative branch lengths is not implemented'
raise HandlingError(msg)
tree.add_branch_lengths()
# do the layout
if fs.daylight:
try:
layout = FastDaylightLayout.StraightBranchLayout()
layout.do_layout(tree)
except RuntimeError as e:
pass
elif fs.curved:
try:
layout = FastDaylightLayout.CurvedBranchLayout()
layout.set_min_segment_count(400)
layout.do_layout(tree)
except RuntimeError as e:
pass
elif fs.arc:
EqualArcLayout.do_layout(tree)
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawTreeImage.get_tree_image(tree, (640, 480), ext)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def do_layout(self, tree):
"""
@param tree: something like a SpatialTree
"""
# create the initial layout
EqualArcLayout.do_layout(tree)
# use sax-like events to create a parallel tree in the C extension
dtree = day.Day()
count = _build_dtree(dtree, tree.root, 0)
# repeatedly reroot and equalize
for iteration in range(self.iteration_count):
for node in tree.breadth_first():
neighbor_count = len(node.children)
if node.parent:
neighbor_count += 1
if neighbor_count > 2:
dtree.select_node(node.dtree_id)
dtree.reroot()
try:
dtree.equalize()
except RuntimeError as e:
raise LayoutError(e)
# extract the x and y coordinates from the parallel tree
for node in tree.preorder():
dtree.select_node(node.dtree_id)
x = dtree.get_x()
y = dtree.get_y()
node.location = (x, y)
# take off the silly dtree_id members
for node in tree.preorder():
del node.dtree_id
def main():
import EqualArcLayout
import Newick
import SpatialTree
# make a spatial tree
tree = Newick.parse(Newick.daylight_example_tree, SpatialTree.SpatialTree)
EqualArcLayout.do_layout(tree)
max_size = (640, 480)
image_formats = ('png', 'pdf', 'ps', 'svg')
for image_format in image_formats:
# get the image string
image_string = get_tree_image(tree, max_size, image_format)
# write the image file
image_filename = 'test.%s' % image_format
with open(image_filename, 'wb') as fout:
fout.write(image_string)
print 'created', image_filename
# write an html file
html_filename = 'test.html'
with open(html_filename, 'w') as fout:
print >> fout, '<html><body>'
for image_format in image_formats:
image_filename = 'test.%s' % image_format
print >> fout, '<a href="%s">%s</a><br/>' % (
image_filename, image_filename)
print >> fout, '</body></html>'
print 'created', html_filename
def do_layout(self, tree):
"""
Interleave the processes of breaking the tree and daylight equalization.
@param tree: something like a SpatialTree
"""
# reroot to a node with more than two neighbors
if get_neighbor_count(tree.root) < 3:
suitable_roots = [
x for x in tree.preorder() if get_neighbor_count(x) > 2]
if suitable_roots:
tree.reroot(suitable_roots[0])
# create the initial layout
EqualArcLayout.do_layout(tree)
# determine the maximum allowed branch length
total_branch_length = tree.get_total_length()
max_branch_length = total_branch_length / float(self.min_segment_count)
# any branch longer than the max branch length will be broken in half
iteration = 0
while True:
print 'progressive iteration', iteration+1
# write the extension tree
dtree = day.Day()
_build_dtree(dtree, tree.root, 0)
# equalize the layout
for node in tree.breadth_first():
if get_neighbor_count(node) > 1:
dtree.select_node(node.dtree_id)
dtree.reroot()
try:
dtree.equalize()
except RuntimeError as e:
raise LayoutError(e)
# read the extension tree
for node in tree.preorder():
dtree.select_node(node.dtree_id)
x = dtree.get_x()
y = dtree.get_y()
node.location = (x, y)
# break the branches
old_nodes = list(tree.preorder())
for node in old_nodes:
if node is tree.root:
if node.blen is not None:
raise HandlingError(
'the root node should not have a branch length')
elif node.blen is None:
raise HandlingError(
'each non-root node should have a branch length')
elif node.blen > max_branch_length:
# create a new node and set its attributes
new = self.node_factory()
new.name = node.name
# insert the new node
tree.insert_node(new, node.parent, node, .5)
# if no node was added then break out of the loop
if len(old_nodes) == len(list(tree.preorder())):
break
else:
iteration += 1
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
tree.assert_valid()
if tree.has_negative_branch_lengths():
msg = 'drawing a tree with negative branch lengths is not implemented'
raise HandlingError(msg)
tree.add_branch_lengths()
# get the dictionary mapping the branch name to the nucleotide
name_to_nucleotide = {}
# parse the column string
for line in iterutils.stripped_lines(fs.column.splitlines()):
name_string, nucleotide_string = SnippetUtil.get_state_value_pair(line)
if nucleotide_string not in list('acgtACGT'):
msg = '"%s" is not a valid nucleotide' % nucleotide_string
raise HandlingError(msg)
nucleotide_string = nucleotide_string.upper()
if name_string in name_to_nucleotide:
raise HandlingError('the name "%s" was duplicated' % name_string)
name_to_nucleotide[name_string] = nucleotide_string
# augment the tips with the nucleotide letters
for name, nucleotide in name_to_nucleotide.items():
try:
node = tree.get_unique_node(name)
except Newick.NewickSearchError as e:
raise HandlingError(e)
if node.children:
msg = 'constraints on internal nodes are not implemented'
raise HandlingError(msg)
node.state = nucleotide
# get the Jukes-Cantor rate matrix object
dictionary_rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix()
ordered_states = list('ACGT')
row_major_rate_matrix = MatrixUtil.dict_to_row_major(
dictionary_rate_matrix, ordered_states, ordered_states)
rate_matrix_object = RateMatrix.RateMatrix(row_major_rate_matrix,
ordered_states)
# simulate the ancestral nucleotides
rate_matrix_object.simulate_ancestral_states(tree)
# simulate a path on each branch
# this breaks up the branch into a linear sequence of nodes and adds color
for node in tree.gen_non_root_nodes():
simulate_branch_path(tree, node)
# do the layout
EqualArcLayout.do_layout(tree)
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawTreeImage.get_tree_image(tree, (640, 480), ext)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
tree.assert_valid()
if tree.has_negative_branch_lengths():
msg = 'drawing a tree with negative branch lengths is not implemented'
raise HandlingError(msg)
tree.add_branch_lengths()
# get the dictionary mapping the branch name to the nucleotide
name_to_nucleotide = {}
# parse the column string
for line in iterutils.stripped_lines(fs.column.splitlines()):
name_string, nucleotide_string = SnippetUtil.get_state_value_pair(line)
if nucleotide_string not in list('acgtACGT'):
msg = '"%s" is not a valid nucleotide' % nucleotide_string
raise HandlingError(msg)
nucleotide_string = nucleotide_string.upper()
if name_string in name_to_nucleotide:
raise HandlingError('the name "%s" was duplicated' % name_string)
name_to_nucleotide[name_string] = nucleotide_string
# augment the tips with the nucleotide letters
for name, nucleotide in name_to_nucleotide.items():
try:
node = tree.get_unique_node(name)
except Newick.NewickSearchError as e:
raise HandlingError(e)
if node.children:
msg = 'constraints on internal nodes are not implemented'
raise HandlingError(msg)
node.state = nucleotide
# get the Jukes-Cantor rate matrix object
dictionary_rate_matrix = RateMatrix.get_jukes_cantor_rate_matrix()
ordered_states = list('ACGT')
row_major_rate_matrix = MatrixUtil.dict_to_row_major(
dictionary_rate_matrix, ordered_states, ordered_states)
rate_matrix_object = RateMatrix.RateMatrix(
row_major_rate_matrix, ordered_states)
# simulate the ancestral nucleotides
rate_matrix_object.simulate_ancestral_states(tree)
# simulate a path on each branch
# this breaks up the branch into a linear sequence of nodes and adds color
for node in tree.gen_non_root_nodes():
simulate_branch_path(tree, node)
# do the layout
EqualArcLayout.do_layout(tree)
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawTreeImage.get_tree_image(tree, (640, 480), ext)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_response_content(fs):
# get a properly formatted newick tree with branch lengths
tree = Newick.parse(fs.tree, SpatialTree.SpatialTree)
tree.assert_valid()
if tree.has_negative_branch_lengths():
msg = 'drawing a tree with negative branch lengths is not implemented'
raise HandlingError(msg)
tree.add_branch_lengths()
# get the dictionary mapping the branch name to the nucleotide
name_to_nt = {}
lines = Util.get_stripped_lines(fs.column.splitlines())
if lines:
name_to_nt = SnippetUtil.get_generic_dictionary(lines, 'name',
'nucleotide', list('acgtACGT'))
# augment the tips with the nucleotide letters
for name, nt in name_to_nt.items():
try:
node = tree.get_unique_node(name)
except Newick.NewickSearchError as e:
raise HandlingError(e)
if node.children:
msg = 'constraints on internal nodes are not implemented'
raise HandlingError(msg)
node.state = nt.upper()
# read the rate matrix
R = fs.matrix
# convert the rate matrix to a rate matrix object
states = list('ACGT')
rate_matrix_object = RateMatrix.RateMatrix(R.tolist(), states)
# simulate the ancestral nucleotides
rate_matrix_object.simulate_ancestral_states(tree)
# simulate a path on each branch
# this breaks up the branch into a linear sequence of nodes and adds color
for node in tree.gen_non_root_nodes():
simulate_branch_path(tree, node, rate_matrix_object)
# do the layout
EqualArcLayout.do_layout(tree)
# draw the image
try:
ext = Form.g_imageformat_to_ext[fs.imageformat]
return DrawTreeImage.get_tree_image(tree, (640, 480), ext)
except CairoUtil.CairoUtilError as e:
raise HandlingError(e)
def get_tikz_lines(newick):
tree = Newick.parse(newick, SpatialTree.SpatialTree)
# layout = FastDaylightLayout.StraightBranchLayout()
# layout.set_iteration_count(20)
# layout.do_layout(tree)
EqualArcLayout.do_layout(tree)
tree.fit((2.0, 2.0))
name_to_location = dict((x.name, tree._layout_to_display(x.location)) for x in tree.preorder())
T, B, N = FtreeIO.newick_to_TBN(newick)
node_lines = []
for v, depth in Ftree.T_to_v_to_centrality(T).items():
x, y = name_to_location[N[v]]
line = get_vertex_line(v, depth, x, y)
node_lines.append(line)
edge_lines = []
for va, vb in T:
line = get_edge_line(va, vb)
edge_lines.append(line)
return node_lines + edge_lines
def get_tikz_lines(newick):
tree = Newick.parse(newick, SpatialTree.SpatialTree)
#layout = FastDaylightLayout.StraightBranchLayout()
#layout.set_iteration_count(20)
#layout.do_layout(tree)
EqualArcLayout.do_layout(tree)
tree.fit((2.0, 2.0))
name_to_location = dict(
(x.name, tree._layout_to_display(x.location)) for x in tree.preorder())
T, B, N = FtreeIO.newick_to_TBN(newick)
node_lines = []
for v, depth in Ftree.T_to_v_to_centrality(T).items():
x, y = name_to_location[N[v]]
line = get_vertex_line(v, depth, x, y)
node_lines.append(line)
edge_lines = []
for va, vb in T:
line = get_edge_line(va, vb)
edge_lines.append(line)
return node_lines + edge_lines
def do_layout(self, tree):
"""
@param tree: something like a SpatialTree
"""
original_root = tree.root
if self.force_straight_branches:
min_adjacent_nodes = 3
else:
min_adjacent_nodes = 2
EqualArcLayout.do_layout(tree)
for i in range(self.iterations):
internal_nodes = list(tree.breadth_first())
#random.shuffle(internal_nodes)
for node in internal_nodes:
adjacent_node_count = 0
if node.parent:
adjacent_node_count += 1
adjacent_node_count += len(node.children)
if adjacent_node_count >= min_adjacent_nodes:
tree.reroot(node)
_equal_daylight(tree)
tree.reroot(original_root)
def do_layout(self, tree):
"""
@param tree: something like a SpatialTree
"""
original_root = tree.root
if self.force_straight_branches:
min_adjacent_nodes = 3
else:
min_adjacent_nodes = 2
EqualArcLayout.do_layout(tree)
for i in range(self.iterations):
internal_nodes = list(tree.breadth_first())
#random.shuffle(internal_nodes)
for node in internal_nodes:
adjacent_node_count = 0
if node.parent:
adjacent_node_count += 1
adjacent_node_count += len(node.children)
if adjacent_node_count >= min_adjacent_nodes:
tree.reroot(node)
_equal_daylight(tree)
tree.reroot(original_root)
def demo():
import EqualArcLayout
import DrawTreeImage
# read a tree
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, SpatialTree)
# do the layout
EqualArcLayout.do_layout(tree)
# show some debugging information
max_size = (640, 480)
tree.fit(max_size)
extents = tree.get_extents()
print 'extents:', extents
branches = list(tree.gen_branches())
print 'branches:'
for branch in branches:
print branch.src_location, branch.dst_location
# draw the image
image_format = 'png'
image_string = DrawTreeImage.get_tree_image(tree, max_size, image_format)
# write the image file
with open('test.%s' % image_format, 'wb') as fout:
fout.write(image_string)
def demo():
import EqualArcLayout
import DrawTreeImage
# read a tree
tree_string = Newick.daylight_example_tree
tree = Newick.parse(tree_string, SpatialTree)
# do the layout
EqualArcLayout.do_layout(tree)
# show some debugging information
max_size = (640, 480)
tree.fit(max_size)
extents = tree.get_extents()
print "extents:", extents
branches = list(tree.gen_branches())
print "branches:"
for branch in branches:
print branch.src_location, branch.dst_location
# draw the image
image_format = "png"
image_string = DrawTreeImage.get_tree_image(tree, max_size, image_format)
# write the image file
with open("test.%s" % image_format, "wb") as fout:
fout.write(image_string)