def color_clade(self, clade_field, clade, color):
""" Will highlight a certain clade by drawing a sector around the clade.
The sector will start at the root of the clade and create an arc from the
most to the right most tip. The sector will aslo have a defualt arc length
equal to the distance from the root of the clade to the deepest tip..
Parameters
----------
clade : string
The clade to highlight
color : string (hex string)
The color to highlight the clade with
Returns
-------
return : list
A list of all highlighted clades
"""
if clade_field != 'None':
c = clade
clade_root = self.edge_metadata.loc[self.edge_metadata[clade_field] == clade]
clade_roots_id = clade_root['Node_id'].values
if len(clade_roots_id) == 0:
for c in range(0, len(self.cached_clades)):
if clade in self.cached_clades[c]:
self.cached_clades[c][clade]['color'] = color
return {"empty": []}
i = 0
for clade_root_id in clade_roots_id:
clades = self.tree.find_all(clade_root_id)
for clade in clades:
color_clade = self.tree.get_clade_info(clade)
color_clade['color'] = color
color_clade_s = tools.create_arc_sector(color_clade)
depth = len([node.name for node in clade.ancestors()])
self.colored_clades[c+str(i)] = {'data': color_clade_s,
'depth': depth,
'color': color,
'node': clade}
i += 1
else:
i = 0
clade_name = clade
for (k,v) in self.colored_clades.items():
if clade_name in k:
clade = v['node']
color_clade = self.tree.get_clade_info(clade)
color_clade['color'] = color
color_clade_s = tools.create_arc_sector(color_clade)
depth = len([node.name for node in clade.ancestors()])
self.colored_clades[k] = {'data': color_clade_s,
'depth': depth,
'color': color,
'node': clade}
i += 1
return self.get_colored_clade()
def refresh_clades(self):
colored_clades = {}
for k, v in self.colored_clades.items():
clade_root = self.edge_metadata.loc[self.edge_metadata[
self.clade_field] == k]
clade_root_id = clade_root['Node_id'].values[0] if len(
clade_root) > 0 else -1
if clade_root_id != -1:
clade = self.tree.find(clade_root_id)
tips = clade.tips()
clade_ancestor = clade.parent
center_coords = (clade.x2, clade.y2)
ancestor_coords = (clade_ancestor.x2 - clade.x2,
clade_ancestor.y2 - clade.y2)
points = [[tip.x2 - clade.x2, tip.y2 - clade.y2]
for tip in tips]
color_clade = tools.sector_info(points, center_coords,
ancestor_coords)
color_clade['color'] = v['color']
color_clade_s = tools.create_arc_sector(color_clade)
depth = len([node.name for node in clade.ancestors()])
colored_clades[k] = {
'data': color_clade_s,
'depth': depth,
'color': color_clade['color']
}
return colored_clades
def refresh_clades(self):
colored_clades = {}
for k, v in self.colored_clades.items():
clade_id = self.colored_clades[k]['id']
clade = self.tree.find(clade_id)
color_clade = self.tree.get_clade_info(clade)
color_clade['color'] = v['color']
color_clade_s = tools.create_arc_sector(color_clade)
depth = len([node.name for node in clade.ancestors()])
colored_clades[k] = {'data': color_clade_s,
'depth': depth,
'color': color_clade['color']}
return colored_clades
def color_clade(self, clade, color):
""" Will highlight a certain clade by drawing a sector around the clade.
The sector will start at the root of the clade and create an arc from the
most to the right most tip. The sector will aslo have a defualt arc length
equal to the distance from the root of the clade to the deepest tip..
Parameters
----------
clade : string
The clade to highlight
color : string (hex string)
The color to highlight the clade with
Returns
-------
return : list
A list of all highlighted clades
"""
# is it be safe to assume clade ids will be unique?
c = clade
clade_root = self.edge_metadata.loc[self.edge_metadata[
self.clade_field] == clade]
clade_root_id = clade_root['Node_id'].values[0] if len(
clade_root) > 0 else -1
if clade_root_id == -1:
for c in range(0, len(self.cached_clades)):
if clade in self.cached_clades[c]:
self.cached_clades[c][clade]['color'] = color
return {"empty": []}
clade = self.tree.find(clade_root_id)
tips = clade.tips()
clade_ancestor = clade.parent
center_coords = (clade.x2, clade.y2)
ancestor_coords = (clade_ancestor.x2 - clade.x2,
clade_ancestor.y2 - clade.y2)
points = [[tip.x2 - clade.x2, tip.y2 - clade.y2] for tip in tips]
color_clade = tools.sector_info(points, center_coords, ancestor_coords)
color_clade['color'] = color
color_clade_s = tools.create_arc_sector(color_clade)
depth = len([node.name for node in clade.ancestors()])
self.colored_clades[c] = {
'data': color_clade_s,
'depth': depth,
'color': color
}
return self.get_colored_clade()
def test_create_arc_sector(self):
tools.NUM_TRI = 1
sector_info = {
'theta': math.pi / 2,
'starting_angle': 0,
'center_x': 0,
'center_y': 0,
'largest_branch': 1,
'color': 'FFFFFF'
}
exp_arc = [0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1]
res_arc = tools.create_arc_sector(sector_info)
for i in range(len(res_arc)):
self.assertEqual(
math.isclose(exp_arc[i], res_arc[i], abs_tol=1e-09), True)