def treelegendtext(whattoprint, color):
text = TextFace(" %s " % whattoprint)
text.hz_align = False
text.fsize = 30
text.fstyle = 'Bold'
text.background.color = color
return text
def treelegendtext(whattoprint, color):
text = TextFace(" %s " % whattoprint)
text.hz_align = False
text.fsize = 30
text.fstyle = 'Bold'
text.background.color = color
return text
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 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 addCoreDataToTree(ete_tree,
runid,
sanitized=False,
any_org=False,
all_org=False,
only_org=False,
none_org=False,
uniq_org=False,
color="Black",
compare_to_adj_clade=False):
'''A function to add data related to gene and organism distribution across clusters
to a core gene tree.
Optionally (with compare_to_adj_clade) instead of comparing to the organisms in the whole tree,
we compare to only the organisms in the sister clade at each node.
See http://etetoolkit.org/docs/latest/reference/reference_treeview.html#color-names for a list
of valid color names.'''
cl = getClusterOrgsByRun(runid)
outgroup = None
nodenum = 0
nodeNumToClusterList = {}
# The strategy really doesn't matter, it's just for aesthetics... and to make sure its always the same.
for node in ete_tree.traverse("postorder"):
nodenum += 1
leafnames = node.get_leaf_names()
if compare_to_adj_clade:
outgroup = []
if node.is_root():
# The root node has no sisters
continue
else:
# This is a list - there can be more than one sister node
sisters = node.get_sisters()
for sister in sisters:
outgroup += sister.get_leaf_names()
pass
pass
pass
clusters = findGenesByOrganismList(leafnames,
runid,
cl=cl,
sanitized=True,
all_org=all_org,
any_org=any_org,
only_org=only_org,
none_org=none_org,
uniq_org=uniq_org,
outgroup=outgroup)
numclusters = len(clusters)
# This is mostly so that I can keep track of progress.
sys.stderr.write("%d (N%d)\n" % (numclusters, nodenum))
numFace = TextFace("%d (N%d)" % (numclusters, nodenum),
ftype="Times",
fsize=24,
fgcolor=color)
node.add_face(numFace, 0, position="branch-bottom")
nodeNumToClusterList[nodenum] = clusters
return ete_tree, nodeNumToClusterList
