def layout(node):
if node.is_leaf():
if "Russia/" in node.name:
Rudesc = faces.AttrFace("name", fsize=10)
Rudesc.margin_left = 25
faces.add_face_to_node(Rudesc, node, 0, aligned=True)
else:
if "_" in node.name:
node.name = node.name.replace("_", " ")
countrydesc = faces.AttrFace("name", fsize=10)
countrydesc.margin_left = 5
countrydesc.margin_bottom = 10
countrydesc.margin_top = 5
countrydesc.margin_right = 5
faces.add_face_to_node(countrydesc, node, 0, aligned=False)
def set_face(ftype, fgcolor, fsize=25):
face = faces.AttrFace("name",
fsize=fsize,
fgcolor=fgcolor,
ftype=ftype)
face.margin_left = 2
return face
# Creates a random tree with 8 leaves using a given set of names
# t.populate(8, ["Dme", "Dre", "Hsa", "Ptr", "Cfa", "Mms"])
# Set the path in which images are located
img_path = "./"
# Create faces based on external images
humanFace = faces.ImgFace(img_path + "human.png")
mouseFace = faces.ImgFace(img_path + "mouse.png")
dogFace = faces.ImgFace(img_path + "dog.png")
chimpFace = faces.ImgFace(img_path + "chimp.png")
fishFace = faces.ImgFace(img_path + "fish.png")
flyFace = faces.ImgFace(img_path + "fly.png")
# Create a faces ready to read the name attribute of nodes
#nameFace = faces.TextFace(open("text").readline().strip(), fsize=20, fgcolor="#009000")
nameFace = faces.AttrFace("name", fsize=20, fgcolor="#009000")
# Create a conversion between leaf names and real names
code2name = {
"Dre": "Drosophila melanogaster",
"Dme": "Danio rerio",
"Hsa": "H**o sapiens",
"Ptr": "Pan troglodytes",
"Mms": "Mus musculus",
"Cfa": "Canis familiaris"
}
# Creates a dictionary with the descriptions of each leaf name
code2desc = {
"Dre":
"""
def tree_renderer(tree, treeid, application):
# The following part controls the features that are attched to
# leaf nodes and that will be shown in the tree image. Node styles
# are set it here, and faces are also created. The idea is the
# following: user can pass feature names using the URL argument
# "tree_features". If the feature is handled by our function and
# it is available in nodes, a face will be created and added to
# the global variable LEAVE_FACES. Remember that our layout
# function uses such variable to add faces to nodes during
# rendering.
# Extracts from URL query the features that must be drawn in the tree
asked_features = application.queries.get("show_features",
["name"])[0].split(",")
print >> sys.stderr, asked_features
def update_features_avail(feature_key, name, col, fsize, fcolor, prefix,
suffix):
text_features_avail.setdefault(
feature_key, [name, 0, col, fsize, fcolor, prefix, suffix])
text_features_avail[feature_key][1] += 1
tree.add_feature("fgcolor", "#833DB4")
tree.add_feature("shape", "sphere")
tree.add_feature("bsize", "8")
tree.dist = 0
# This are the features that I wanto to convert into image
# faces. I use an automatic function to do this. Each element in
# the dictionary is a list that contains the information about how
# to create a textFace with the feature.
leaves = tree.get_leaves()
formated_features = {
# feature_name: ["Description", face column position, text_size, color, text_prefix, text_suffix ]
"name": ["Leaf name",
len(leaves), 0, 12, "#000000", "", ""],
"spname":
["Species name",
len(leaves), 1, 12, "#f00000", " Species:", ""],
}
# populates the global LEAVE_FACES variable
global LEAVE_FACES
LEAVE_FACES = []
unknown_faces_pos = 2
for fkey in asked_features:
if fkey in formated_features:
name, total, pos, size, color, prefix, suffix = formated_features[
fkey]
f = faces.AttrFace(fkey,
ftype="Arial",
fsize=size,
fgcolor=color,
text_prefix=prefix,
text_suffix=suffix)
LEAVE_FACES.append([f, fkey, pos])
else:
# If the feature has no associated format, let's add something standard
prefix = " %s: " % fkey
f = faces.AttrFace(fkey,
ftype="Arial",
fsize=10,
fgcolor="#666666",
text_prefix=prefix,
text_suffix="")
LEAVE_FACES.append([f, fkey, unknown_faces_pos])
unknown_faces_pos += 1
text_features_avail = {}
for l in leaves:
for f in l.features:
if not f.startswith("_"):
text_features_avail.setdefault(f, 0)
text_features_avail[f] = text_features_avail[f] + 1
html_features = """
<div id="tree_features_box">
<div class="tree_box_header">Available tree features
<img src="/webplugin/close.png" onclick='$(this).closest("#tree_features_box").hide();'>
</div>
<form action='javascript: set_tree_features("", "", "");'>
"""
for fkey, counter in text_features_avail.iteritems():
if fkey in asked_features:
tag = "CHECKED"
else:
tag = ""
fname = formated_features.get(fkey, [fkey])[0]
#html_features = "<tr>"
html_features += '<INPUT NAME="tree_feature_selector" TYPE=CHECKBOX %s VALUE="%s">%s (%s/%s leaves)</input><br> ' %\
(tag, fkey, fname, counter, len(leaves))
# html_features += '<td><INPUT size=7 type="text"></td> <td><input size=7 type="text"></td> <td><input size=7 type="text"></td> <td><input size=1 type="text"></td><br>'
#html_features += "</tr>"
html_features += """<input type="submit" value="Refresh"
onclick='javascript:
// This piece of js code extracts the checked features from menu and redraw the tree sending such information
var allVals = [];
$(this).parent().children("input[name=tree_feature_selector]").each(function(){
if ($(this).is(":checked")){
allVals.push($(this).val());
}});
draw_tree("%s", "", "#img1", {"show_features": allVals.join(",")} );'
>
</form></div>""" % (treeid)
features_button = """
<li><a href="#" onclick='show_box(event, $(this).closest("#tree_panel").children("#tree_features_box"));'>
<img width=16 height=16 src="/webplugin/icon_tools.png" alt="Select Tree features">
</a></li>"""
download_button = """
<li><a href="/webplugin/tmp/%s.png" target="_blank">
<img width=16 height=16 src="/webplugin/icon_attachment.png" alt="Download tree image">
</a></li>""" % (treeid)
search_button = """
<li><a href="#" onclick='javascript:
var box = $(this).closest("#tree_panel").children("#search_in_tree_box");
show_box(event, box); '>
<img width=16 height=16 src="/webplugin/icon_search.png" alt="Search in tree">
</a></li>"""
clean_search_button = """
<li><a href="#" onclick='run_action("%s", "", %s, "clean::clean");'>
<img width=16 height=16 src="/webplugin/icon_cancel_search.png" alt="Clear search results">
</a></li>""" %\
(treeid, 0)
buttons = '<div id="ete_tree_buttons">' +\
features_button + search_button + clean_search_button + download_button +\
'</div>'
search_select = '<select id="ete_search_target">'
for fkey in text_features_avail:
search_select += '<option value="%s">%s</option>' % (fkey, fkey)
search_select += '</select>'
search_form = """
<div id="search_in_tree_box">
<div class="tree_box_header"> Search in Tree
<img src="/webplugin/close.png" onclick='$(this).closest("#search_in_tree_box").hide();'>
</div>
<form onsubmit='javascript:
search_in_tree("%s", "%s",
$(this).closest("form").children("#ete_search_term").val(),
$(this).closest("form").children("#ete_search_target").val());'
action="javascript:void(0);">
%s
<input id="ete_search_term" type="text" value=""'></input>
<br><i>(Searches are not case sensitive and accept Perl regular expressions)</i>
<br>
</form>
<i> (Press ENTER to initiate the search)</i>
</div>
""" %\
(treeid, 0, search_select) # 0 is the action index associated
# to the search functionality. This
# means that this action is the
# first to be registered in WebApplication.
tree_panel_html = '<div id="tree_panel">' + search_form + html_features + buttons + '</div>'
# Now we render the tree into image and get the HTML that handles it
tree_html = application._get_tree_img(treeid=treeid)
# Let's return enriched HTML
return tree_panel_html + tree_html
def layout(node):
name_face = faces.AttrFace("name", fsize=10, fgcolor="#009000")
# If node is a leaf, add the node name
if node.is_leaf():
faces.add_face_to_node(name_face, node, column=0)
faces.add_face_to_node(AttrFace("node_id"), node, column=0)
def test(node):
if node.is_leaf():
faces.add_face_to_node(faces.AttrFace("name"),
node,
0,
position="aligned")
def leaf_name(node):
if node.is_leaf():
nameF = faces.AttrFace("name")
nameF.border.width = 1
faces.add_face_to_node(nameF, node, 0, position="branch-right")
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
elif opt == '-u':
ultrametric = int(arg)
elif opt == '-s':
support_threshold = float(arg)
elif opt == '-i':
show_IDs = int(arg)
gene_tree = args[0]
print(gene_tree)
print(gene_format)
gene_tree = Tree(gene_tree, format=gene_format)
#gene_tree = ete2.Tree("/home/ciach/Projects/Tree_node_classification/Comparison_with_Notung/Sequences/ABV48733.1/decomposed_tree.dnd")
#species_tree = ete2.Tree("/home/ciach/Projects/Tree_node_classification/Comparison_with_Notung/Sequences/ABV48733.1/species_tree.dnd")
suppFace = faces.AttrFace("support",
text_suffix=" ",
formatter="%.2f",
fsize=8)
iFace = faces.AttrFace("I", fsize=8, text_suffix='/')
pFace = faces.AttrFace("P", fsize=8, text_suffix=' ')
idFace = faces.AttrFace("id", fsize=8)
for i, g in enumerate(gene_tree.traverse(strategy="postorder")):
g.id = i
#g.name = g.name.split('_')[0]
g.coloured = False
g.nw = g.source
g.source = True if g.source == 'True' else False
g.dist = 1.0
if hasattr(g, 'I'):
if g.I == "None":
g.I = -1
else:
array = t.arraytable
# Calculates some stats on the matrix
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = faces.ProfileFace(matrix_max, matrix_min, matrix_avg, \
200, 14, "heatmap")
cbarsFace = faces.ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 70,
"cbars")
nameFace = faces.AttrFace("name", fsize=8)
# 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
faces.add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
faces.add_face_to_node(nameFace, node, 1, aligned=True)
# If node is internal
else:
# If silhouette is good, creates a green bubble
if node.silhouette > 0: