def style_and_render_tree(self, file_types=["svg"]):
from ete3 import TreeStyle, TextFace, CircleFace
ts = TreeStyle()
title_face = TextFace(f"{genus} {snakemake.config['species']}", fsize=20)
title_face.margin_bottom = 10
ts.title.add_face(title_face, column=0)
ts.branch_vertical_margin = 10
ts.show_leaf_name = True
# Legend
ts.legend.add_face(TextFace(""), column=1)
for category in ["Allowed", "Deviations", "Filtered", "Color"]:
category = TextFace(category, fsize=8, bold=True)
category.margin_bottom = 2
category.margin_right = 40
ts.legend.add_face(category, column=1)
for i, criteria in enumerate(CRITERIA, 2):
title = criteria.replace("_", " ").title()
title = TextFace(title, fsize=8, bold=True)
title.margin_bottom = 2
title.margin_right = 40
cf = CircleFace(4, COLORS[criteria], style="sphere")
cf.margin_bottom = 5
filtered_count = len(
list(filter(None, self.failed_report.criteria == criteria))
)
filtered = TextFace(filtered_count, fsize=8)
filtered.margin_bottom = 5
allowed = TextFace(self.allowed[criteria], fsize=8)
allowed.margin_bottom = 5
allowed.margin_right = 25
# TODO Prevent tolerance from rendering as a float
tolerance = TextFace(self.tolerance[criteria], fsize=8)
tolerance.margin_bottom = 5
ts.legend.add_face(title, column=i)
ts.legend.add_face(allowed, column=i)
ts.legend.add_face(tolerance, column=i)
ts.legend.add_face(filtered, column=i)
ts.legend.add_face(cf, column=i)
for f in file_types:
out_tree = os.path.join(self.paths.qc, "tree.{}".format(f))
self.tree.render(out_tree, tree_style=ts)
def sel_mylayout(node):
node.set_style(my_node_style)
if node.is_leaf():
# add names in larger font + italics
species_name = AttrFace("name", fsize=12, fstyle="italic")
add_face_to_node(species_name,
node,
column=0,
position="branch-right")
# add absence/presence matrix
for i, value in enumerate(getattr(node, "profile", [])):
if value > 0:
color = "#FF0000"
else:
color = "#EEEEEE"
my_face = CircleFace(8, color, style="circle")
my_face.margin_right = 3
my_face.margin_bottom = 3
add_face_to_node(my_face, node, position="aligned", column=i)
def style_and_render_tree(self, file_types=["svg"]):
from ete3 import TreeStyle, TextFace, CircleFace
ts = TreeStyle()
title_face = TextFace(self.name.replace('_', ' '), fsize=20)
title_face.margin_bottom = 10
ts.title.add_face(title_face, column=0)
ts.branch_vertical_margin = 10
ts.show_leaf_name = False
# Legend
ts.legend.add_face(TextFace(""), column=1)
for category in ["Allowed", "Tolerance", "Filtered", "Color"]:
category = TextFace(category, fsize=8, bold=True)
category.margin_bottom = 2
category.margin_right = 40
ts.legend.add_face(category, column=1)
for i, criteria in enumerate(self.criteria, 2):
title = criteria.replace("_", " ").title()
title = TextFace(title, fsize=8, bold=True)
title.margin_bottom = 2
title.margin_right = 40
cf = CircleFace(4, self.colors[criteria], style="sphere")
cf.margin_bottom = 5
filtered_count = len(
list(filter(None, self.failed_report.criteria == criteria)))
filtered = TextFace(filtered_count, fsize=8)
filtered.margin_bottom = 5
allowed = TextFace(self.allowed[criteria], fsize=8)
allowed.margin_bottom = 5
allowed.margin_right = 25
tolerance = TextFace(self.tolerance[criteria], fsize=8)
tolerance.margin_bottom = 5
ts.legend.add_face(title, column=i)
ts.legend.add_face(allowed, column=i)
ts.legend.add_face(tolerance, column=i)
ts.legend.add_face(filtered, column=i)
ts.legend.add_face(cf, column=i)
for f in file_types:
out_tree = os.path.join(self.qc_results_dir, 'tree.{}'.format(f))
self.tree.render(out_tree, tree_style=ts)
self.log.info("tree.{} generated".format(f))