def plot_phylo(nw_tree,
out_name,
parenthesis_classif=True,
show_support=False,
radial_mode=False,
root=False):
from ete3 import Tree, AttrFace, TreeStyle, NodeStyle, TextFace
import orthogroup2phylogeny_best_refseq_uniprot_hity
ete2_tree = Tree(nw_tree, format=0)
if root:
R = ete2_tree.get_midpoint_outgroup()
# and set it as tree outgroup
ete2_tree.set_outgroup(R)
ete2_tree.set_outgroup('Bacillus subtilis')
ete2_tree.ladderize()
if parenthesis_classif:
print('parenthesis_classif!')
name2classif = {}
for lf in ete2_tree.iter_leaves():
print(lf)
try:
classif = lf.name.split('_')[-2][0:-1]
print('classif', classif)
#lf.name = lf.name.split('(')[0]
name2classif[lf.name] = classif
except:
pass
classif_list = list(set(name2classif.values()))
classif2col = dict(
zip(
classif_list,
orthogroup2phylogeny_best_refseq_uniprot_hity.
get_spaced_colors(len(classif_list))))
for lf in ete2_tree.iter_leaves():
#try:
if parenthesis_classif:
try:
col = classif2col[name2classif[lf.name]]
except:
col = 'black'
else:
col = 'black'
#print col
#lf.name = '%s|%s-%s' % (lf.name, accession2name_and_phylum[lf.name][0],accession2name_and_phylum[lf.name][1])
if radial_mode:
ff = AttrFace("name", fsize=12, fstyle='italic')
else:
ff = AttrFace("name", fsize=12, fstyle='italic')
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
if not show_support:
print('support')
for n in ete2_tree.traverse():
print(n.support)
nstyle = NodeStyle()
if float(n.support) < 1:
nstyle["fgcolor"] = "red"
nstyle["size"] = 4
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
else:
for n in ete2_tree.traverse():
nstyle = NodeStyle()
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
#nameFace = AttrFace(lf.name, fsize=30, fgcolor=phylum2col[accession2name_and_phylum[lf.name][1]])
#faces.add_face_to_node(nameFace, lf, 0, position="branch-right")
#
#nameFace.border.width = 1
'''
except:
col = 'red'
print col
lf.name = '%s| %s' % (lf.name, locus2organism[lf.name])
ff = AttrFace("name", fsize=12)
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
'''
#n = TextFace(lf.name, fgcolor = "black", fsize = 12, fstyle = 'italic')
#lf.add_face(n, 0)
'''
for n in ete2_tree.traverse():
nstyle = NodeStyle()
if n.support < 90:
nstyle["fgcolor"] = "black"
nstyle["size"] = 4
n.set_style(nstyle)
else:
nstyle["fgcolor"] = "red"
nstyle["size"] = 0
n.set_style(nstyle)
'''
ts = TreeStyle()
ts.show_leaf_name = False
#ts.scale=2000
#ts.scale=20000
ts.show_branch_support = show_support
if radial_mode:
ts.mode = "c"
ts.arc_start = -90
ts.arc_span = 360
ts.tree_width = 370
ts.complete_branch_lines_when_necessary = True
ete2_tree.render(out_name, tree_style=ts, w=900)
def ete_layout(node):
"""
Formatting of tree nodes while tree is rendered
:param node: ete node
"""
nstyle = NodeStyle()
nstyle["shape"] = "sphere"
nstyle["size"] = 0
nstyle["vt_line_width"] = 1 # line width of vertical branches
nstyle["hz_line_width"] = 1 # line width of horizontal branches
node.set_style(nstyle)
if 'median_vaf' in node.features and not np.isnan(
node.median_vaf) and logger.isEnabledFor(logging.DEBUG):
# # Creates a sphere face whose size is proportional to the given VAF or CCF of the acquired muts
# cf = CircleFace(radius=node.median_vaf*50, color="RoyalBlue", style="sphere")
# # Let's make the sphere transparent
# cf.opacity = 0.6
# # And place as a float face over the tree
# faces.add_face_to_node(cf, node, column=0, position="float-behind")
vaf_face = TextFace('({:.0%}) '.format(node.median_vaf),
fsize=9,
fgcolor='SlateGray')
vaf_face.opacity = 0.8 # from 0 to 1
faces.add_face_to_node(vaf_face, node, column=2, position="branch-top")
if node.is_root():
# tf_root = TextFace(node.name, fsize=14, fgcolor="Black")
# tf_root.margin_bottom = 25
# faces.add_face_to_node(tf_root, node, column=0, position='branch-right')
return
bt_face_muts = AttrFace("dist",
fsize=11,
fgcolor="Black",
text_prefix=' ',
text_suffix=' ',
formatter='%d')
bt_face_muts.margin_bottom = 2
bt_face_muts.margin_top = 2
faces.add_face_to_node(bt_face_muts, node, column=1, position="branch-top")
if 'drivers' in node.features and len(node.drivers) > 0:
drivers_face = TextFace(node.drivers,
fsize=11,
fstyle='italic',
fgcolor='OrangeRed')
drivers_face.opacity = 0.8 # from 0 to 1
drivers_face.margin_left = 1
drivers_face.margin_right = 1
faces.add_face_to_node(drivers_face,
node,
column=0,
position="branch-top")
# If node is a leaf, add the nodes name and a its scientific name
if node.is_leaf():
# for colors see: http://etetoolkit.org/docs/latest/reference/reference_treeview.html#color-names
leaf_face = AttrFace("name",
fsize=14,
fgcolor="Black",
text_prefix=' ',
text_suffix=' ')
if node.name.startswith('PT') or node.name.startswith(
'Primary'): # primary tumor sample
leaf_face.fgcolor = 'SteelBlue'
elif node.name.startswith('LiM'): # liver met
leaf_face.fgcolor = 'DarkOliveGreen'
elif node.name.startswith('LuM'): # lung met
leaf_face.fgcolor = 'SaddleBrown'
elif node.name.startswith('NoM'): # lymph node met
leaf_face.fgcolor = 'DarkViolet'
elif node.name.startswith('PeM'): # peritoneal met
leaf_face.fgcolor = 'Purple'
elif node.name.startswith('Met') or node.name.startswith(
'M'): # some metastasis
leaf_face.fgcolor = 'Magenta'
elif node.name.startswith('BrM'): # brain met
leaf_face.fgcolor = 'Crimson'
leaf_face.border.type = 0
leaf_face.border.width = 1
leaf_face.margin_bottom = 1
leaf_face.margin_top = 1
faces.add_face_to_node(leaf_face, node,
column=1) # , position="aligned"
else: # inner node
# if not np.isnan(node.support):
# bt_face_conf = AttrFace("support", fsize=12, fgcolor="DimGrey", text_prefix=' ',
# text_suffix=' ', formatter='%0.2f')
if node.confidence is not None and node.confidence != '':
tf_conf = TextFace(node.confidence, fsize=12, fgcolor='DimGrey')
tf_conf.margin_left = 3
tf_conf.margin_right = 3
faces.add_face_to_node(tf_conf,
node,
column=1,
position="branch-bottom")
def plot_tree(ete3_tree,
orthogroup,
biodb,
mysql_host="localhost",
mysql_user="******",
mysql_pwd="baba",
mysql_db="blastnr"):
import MySQLdb
import manipulate_biosqldb
from ete3 import Tree, TreeStyle, faces, AttrFace
conn = MySQLdb.connect(
host=mysql_host, # your host, usually localhost
user=mysql_user, # your username
passwd=mysql_pwd, # your password
db=mysql_db) # name of the data base
cursor = conn.cursor()
locus_list = [lf.name for lf in ete3_tree.iter_leaves()]
filter = '"' + '","'.join(locus_list) + '"'
print('get uniprot taxnomy')
sql1 = 'select subject_accession,subject_scientific_name,t2.phylum from blast_swissprot_%s t1 ' \
' inner join blastnr_taxonomy as t2 on t1.subject_taxid=t2.taxon_id where subject_accession in (%s);' % (biodb,
filter)
sql1 = 'select subject_accession,subject_scientific_name,t4.phylum from biosqldb.orthology_detail_%s t1 ' \
' inner join custom_tables.locus2seqfeature_id_%s t2 ' \
' on t1.locus_tag=t2.locus_tag ' \
' inner join blast_swissprot_%s t3 on t2.seqfeature_id=t3.seqfeature_id ' \
' inner join blastnr_taxonomy as t4 on t3.subject_taxid=t4.taxon_id ' \
' where t1.orthogroup="%s"' % (biodb,
biodb,
biodb,
orthogroup)
print('get refseq taxonomy')
cursor.execute(sql1, )
accession2name_and_phylum = manipulate_biosqldb.to_dict(cursor.fetchall())
sql2 = 'select subject_accession,subject_scientific_name,t4.phylum from biosqldb.orthology_detail_%s t1 ' \
' inner join custom_tables.locus2seqfeature_id_%s t2 ' \
' on t1.locus_tag=t2.locus_tag ' \
' inner join blastnr_%s t3 on t2.seqfeature_id=t3.seqfeature_id ' \
' inner join blastnr_taxonomy as t4 on t3.subject_taxid=t4.taxon_id ' \
' where t1.orthogroup="%s"' % (biodb,
biodb,
biodb,
orthogroup)
print(sql2)
cursor.execute(sql2, )
accession2name_and_phylum.update(
manipulate_biosqldb.to_dict(cursor.fetchall()))
print('plotting tree')
phylum_list = list(
set([
accession2name_and_phylum[i][1]
for i in accession2name_and_phylum.keys()
]))
sql = 'select locus_tag, organism from biosqldb.orthology_detail_%s' % biodb
cursor.execute(sql, )
locus2organism = manipulate_biosqldb.to_dict(cursor.fetchall())
phylum2col = dict(zip(phylum_list, get_spaced_colors(len(phylum_list))))
R = ete3_tree.get_midpoint_outgroup()
# and set it as tree outgroup
ete3_tree.set_outgroup(R)
for lf in ete3_tree.iter_leaves():
try:
col = phylum2col[accession2name_and_phylum[lf.name][1]]
lf.name = '%s|%s-%s' % (lf.name,
accession2name_and_phylum[lf.name][0],
accession2name_and_phylum[lf.name][1])
ff = AttrFace("name", fsize=12)
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
#nameFace = AttrFace(lf.name, fsize=30, fgcolor=phylum2col[accession2name_and_phylum[lf.name][1]])
#faces.add_face_to_node(nameFace, lf, 0, position="branch-right")
#
#nameFace.border.width = 1
except:
col = 'red'
try:
lf.name = '%s| %s' % (lf.name, locus2organism[lf.name])
except:
lf.name = '%s| ??' % (lf.name)
ff = AttrFace("name", fsize=12)
#ff.background.color = 'red'
ff.fgcolor = col
lf.add_face(ff, column=0)
ts = TreeStyle()
ts.show_leaf_name = False
ts.show_branch_support = True
return ete3_tree, ts