def get_tree_style(tree_file, abund, rownames):
with open("matrix.txt", "w") as temp:
cols = len(abund[0])
header = "#Names"
for i in xrange(cols):
header += "\tOTU%d" % i
temp.write("%s\n" % header)
for i, row in enumerate(abund):
temp.write("%s\t%s\n" % (rownames[i], '\t'.join([str(i) for i in row])))
t = Tree(tree_file)
t.convert_to_ultrametric(10)
assert isinstance(abund, numpy.ndarray)
assert isinstance(rownames, numpy.ndarray)
ts = TreeStyle()
ts.mode = "r"
ts.show_leaf_name = False
ts.show_scale = False
ts.show_branch_length = False
ts.branch_vertical_margin = 20
ts.force_topology = True
ts.optimal_scale_level = "full"
ts.scale = 50
ts.draw_guiding_lines = True
ts.guiding_lines_type = 0
ts.guiding_lines_color = "black"
for n in t.traverse():
if not n.is_leaf():
nstyle = NodeStyle()
n.set_style(nstyle)
nstyle['size'] = 0
nstyle['hz_line_width'] = 3
nstyle['vt_line_width'] = 3
else:
nstyle = NodeStyle()
n.set_style(nstyle)
nstyle['size'] = 0
nstyle['hz_line_width'] = 3
nstyle['vt_line_width'] = 3
nstyle['fgcolor'] = "Black"
nstyle['shape'] = "square"
name_face = AttrFace("name", fsize=14, ftype="Arial", fgcolor="black", penwidth=10, text_prefix=" ", text_suffix=" ")
n.add_face(name_face, column=0, position="aligned")
row_index = rownames.tolist().index(n.name)
col = 1
for i in xrange(10):
col += 1
n.add_face(CircleFace(5, color=get_color(abund, row_index, i)), column=col, position="aligned")
return t, ts
def setTreeStyle(style, layoutfunction):
#consolidate options for showing trees
#pass in string "circle" or "rect" and a layout function
I = TreeStyle()
if style == "circle":
I.tree_width = 1200
I.layout_fn = layoutfunction
I.show_branch_length = False
#I.show_branch_support = True
I.show_leaf_name = False
I.mode = "c"
I.force_topology = True
#I.legend_position = 3
I.extra_branch_line_type = 1
I.guiding_lines_type = 1
I.guiding_lines_color = "#666666"
I.extra_branch_line_color = "#666666"
I.optimal_scale_level = "full"
I.root_opening_factor = 0
elif style =="rect":
I = TreeStyle()
I.layout_fn = layoutfunction
I.show_leaf_name = False
I.force_topology = True
I.optimal_scale_level = "semi"
else:
I.layout_fn = layoutfunction
I.show_leaf_name = False
I.force_topology = True
I.optimal_scale_level = "semi"
return I
from ete2 import EvolTree
from ete2 import faces
tree = EvolTree("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment("data/S_example/alignment_S_measuring_evol.fasta")
print tree
print "\n Running free-ratio model with calculation of ancestral sequences..."
tree.run_model("fb_anc")
# tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc')
I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id):
if n.is_leaf():
continue
anc_face = faces.SequenceFace(n.sequence, "aa", fsize=10, bg_colors={})
I.aligned_foot.add_face(anc_face, 1)
I.aligned_foot.add_face(faces.TextFace("node_id: #%d " % (n.node_id), fsize=8), 0)
print "display result of bs_anc model, with ancestral amino acid sequences."
tree.show(tree_style=I)
print "\nThe End."
def doWork(args):
# read clustering data
geneIdToClusterId = {}
clusterIds = []
for line in open(args.cluster):
if line[0] == '%':
clusterId = line[1:].strip()
clusterIds.append(clusterId)
else:
geneIdToClusterId[line.strip()] = clusterId
# create colour map for clusters
clusterIdToColour = {}
index = 0
for clusterId in clusterIds:
rgb = tuple([int(c*255) for c in hsv_to_rgb(float(index)/len(clusterIds), 0.4, 1.0)])
clusterIdToColour[clusterId] = '#%02X%02X%02X' % rgb
index += 1
# read tree
tree = Tree(args.tree)
# define node properties
for node in tree.traverse('levelorder'):
if node.is_leaf():
name = node.name.replace("'", '')
clusterId = geneIdToClusterId[name]
node.add_feature('clusterId', clusterId)
if args.label:
node.name = ' ' + name + ' [' + clusterId + ']'
ns = NodeStyle()
ns['shape'] = 'circle'
ns['fgcolor'] = 'black'
ns['size'] = 4
node.set_style(ns)
else:
ns = NodeStyle()
ns['size'] = 0
node.set_style(ns)
# determine colour for each node
assignedColor = set()
for node in tree.traverse('levelorder'):
if node.is_leaf() or node.is_root():
continue
# determine clusters descendent from this node
clusterSet = set()
for leaf in node.get_leaves():
clusterSet.add(leaf.clusterId)
# check if parent has already been assigned a colour
bContinue = False
parentNode = node.up
while not parentNode.is_root():
if parentNode in assignedColor:
bContinue = True
break
parentNode = parentNode.up
if bContinue:
continue
# colour node if all descendants are from the same cluster
if len(clusterSet) == 1:
clusters = list(clusterSet)
ns = NodeStyle()
ns['bgcolor'] = clusterIdToColour[clusters[0]]
ns['size'] = 0
node.set_style(ns)
assignedColor.add(node)
# create tree style for plotting consisteny index trees
treeStyle = TreeStyle()
treeStyle.margin_left = 10
treeStyle.margin_right = 10
treeStyle.margin_top = 10
treeStyle.margin_bottom = 10
treeStyle.guiding_lines_type = 1
treeStyle.legend_position=1
treeStyle.scale = 500
# add legend
rowIndex = 0
for clusterId in sorted(clusterIdToColour.keys()):
treeStyle.legend.add_face(CircleFace(4, clusterIdToColour[clusterId]), column=0)
treeStyle.legend.add_face(TextFace(' ' + clusterId), column=1)
rowIndex += 1
tree.render(args.output, dpi=args.dpi, w = int(args.width*args.dpi + 0.5), tree_style=treeStyle)
