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 show(self, layout=None, tree_style=None, histfaces=None):
'''
call super show of PhyloTree
histface should be a list of models to be displayes as histfaces
:argument layout: a layout function
:argument None tree_style: tree_style object
:argument Nonehistface: an histogram face function. This is only to plot selective pressure among sites
'''
if TREEVIEW:
if not tree_style:
ts = TreeStyle()
else:
ts = tree_style
if histfaces:
for hist in histfaces:
try:
mdl = self.get_evol_model(hist)
except AttributeError:
warn('model %s not computed' % (hist))
if not 'histface' in mdl.properties:
if len(histfaces) > 1 and histfaces.index(hist) != 0:
mdl.set_histface(up=False)
else:
mdl.set_histface()
if mdl.properties['histface'].up:
ts.aligned_header.add_face(mdl.properties['histface'],
1)
else:
ts.aligned_foot.add_face(mdl.properties['histface'], 1)
super(EvolTree, self).show(layout=layout, tree_style=ts)
else:
raise ValueError("Treeview module is disabled")
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
if options.gene is None:
gene = options.clusterrunid
else:
gene = options.gene
# FIXME - if we declare this as a PhyloTree rather than just a Tree, ETE for some reason creates an
# EXTRA COPY of the names (try it and see!) and therefore if you set show_leaf_names to True it shows
# TWO copies of the leaf name at each leaf node (and if you set it to False it shows one, making it look
# like it's ignoring you when you set it to False). The Tree class works as expected.
#
# Since we only need PhyloTree when we want to export to PhyloXML (not implemented yet), we should only create one
# in that instance (due to the brokenness)
# t = PhyloTree(treeinfile, sp_naming_function=parse_sp_name)
t = Tree(treeinfile)
ts = TreeStyle()
con = sqlite3.connect(locateDatabase())
cur = con.cursor()
tempdir = tempfile.mkdtemp()
t, ts = draw_tree_regions(clusterrunid,
t,
ts,
cur,
greyout=options.cutoff,
tempdir=tempdir,
label=options.label)
# Now that we don't need to reference anything with the gene IDs any more, try to change them into
# FIXME - This should call the library functions to get geneinfo for specific sets of genes
# instead of doing this.
con = sqlite3.connect(locateDatabase())
cur = con.cursor()
cur.execute("SELECT * FROM processed;")
for l in cur:
spl = [ str(s) for s in list(l) ]
# The SVG parser whines with some special characters (i.e. ' )
# I use the sanitized version as a key here so that the code will work whether or not the leaf names
# have been sanitized in the input tree.
geneToAnnote[sanitizeString(spl[0], False)] = sanitizeString(spl[9], False)
geneToOrganism[sanitizeString(spl[0], False)] = sanitizeString(spl[1], False)
ts = TreeStyle()
# Now we try and add the heatmap
# if the user requests it
#
# I borrowed some of this code from the ETE tutorial.
if options.datafile is not None:
array = t.arraytable
numcols = len(array.colNames)
matrix_dist = [i for r in range(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)
# Max, Min, Center, Width, Height, Type)
