def layout(node):
node.img_style["size"] = 5
node.img_style["hz_line_width"] = 0
node.img_style["vt_line_width"] = 0
if node.is_leaf():
f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
faces.add_face_to_node(f, node, 0, position="aligned")
f = faces.AttrFace("name", fsize=15)
faces.add_face_to_node(f, node, 0, position="branch-right")
else:
f = faces.TextFace("uno", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-top")
f = faces.TextFace("otromassssssssssss", fsize=8)
for x in xrange(random.randint(1, 5)):
faces.add_face_to_node(f, node, 0, position="branch-bottom")
f = faces.CircleFace(20, "red")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float")
f = faces.CircleFace(23, "blue")
f.opacity = 0.3
faces.add_face_to_node(f, node, 0, position="float-behind")
def prettifyTree(ete_tree,
leaf_font_size=32,
branch_support_size=20,
show_bootstraps=True,
title=None,
ts=None):
''' Perform standardized functions to make the ETE trees easier to read:
- Make the branch support bigger
- Make the leaf fonts bigger
- Turn off elongating branches for visualization purposes (i.e. make sure the real branch lengths are represented)
- Change both to standard font (Times)
- Standardize the tree's width (calculate based on the maximum length from the root to a tip)
- (optional) add title to tree
'''
for node in ete_tree.traverse():
if node.is_leaf():
# Make text faces with name = the existing node name but with big font.
# A side effect of this is that we also get the annotations lined up
F = faces.TextFace(node.name, ftype="Times", fsize=leaf_font_size)
node.add_face(F, 0, position="aligned")
else:
if show_bootstraps:
# Make branch support bigger
F = faces.TextFace(node._support,
ftype="Times",
fsize=branch_support_size)
node.add_face(F, 0, position="branch-top")
#correct the long root node bug (fixed in next release)
ete_tree.dist = 0
# Optionally create a new TreeStyle if we are not passing in an old one.
if ts is None:
ts = TreeStyle()
# This "fixes" the dashed line issue but makes the tree look terrible.
# There may be no way around this (and it's likely other tree viewers do the same thing
# but just don't tell you).
#ts.optimal_scale_level = "full"
# We made these bigger so lets turn off the default ones too.
ts.show_branch_support = False
ts.show_leaf_name = False
if title is not None:
ts.title.clear()
title = TextFace(title)
title.hz_align = True
title.fsize = 52
ts.title.add_face(title, 0)
return ete_tree, ts
def layout(node):
node.img_style["size"] = random.randint(5,100)
node.img_style["hz_line_width"] = 5
node.img_style["vt_line_width"] = 10
if node.is_leaf():
#node.img_style["size"] = random.randint(50, 50)
f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
#f = faces.AttrFace("name", fsize=random.randint(20,20))
faces.add_face_to_node(f, node, 0, position="aligned")
f.border.width = 0
#f = faces.CircleFace(20, "red")
#f = faces.AttrFace("name", fsize=20)
f = faces.TextFace("NAME", fsize=10)
#faces.add_face_to_node(f, node, 0, position="branch-right")
f.border.width = 0
# Max, Min, Center, Width, Height, Type)
# I give it 60 pixels per column by default
# (so that the width doesn't shrink down too much when we have more than a few columns)
# However, the user has the ability to change thsi if they need to / want to for larger data sets
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, width=numcols*options.data_width, height=35, style="heatmap")
for node in t.traverse():
if node.is_leaf():
node.add_face(profileFace, 1, position = "aligned")
# Add the color bar (kind of hacked in from matplotlib since there is no convenient way to get it from ETE)
# I could generate this in situ... for now I just have a file I like and run with it.
# This doesn't match exactlty becuase I don't have the time or motivation now to mess with QT to do it.
# It should be pretty close though...
from ete2 import ImgFace
imgloc = os.path.join(locateRootDirectory(), "src", "internal", "Colormap.png")
F1 = faces.TextFace("Minimum: %1.1f" %(matrix_min), ftype="Times", fsize=32 )
F2 = faces.ImgFace(imgloc)
F3 = faces.TextFace("%1.1f : Maximum" %(matrix_max), ftype="Times", fsize=32 )
ts.legend.add_face(F1, 0)
ts.legend.add_face(F2, 1)
ts.legend.add_face(F3, 2)
# Put it on the Bottom-left
ts.legend_position = 3
if options.savenewick:
t.write(outfile="%s.nwk" %(options.basename), format=0)
if options.savesvg:
# Some versions of ETE create a "test.svg" and others do not.
# To avoid confusion (and in case TreeStyle isn't enforced)
# I just create a new one.