def draw_branch_mark(arg,
layout,
node=None,
parent=None,
pos=None,
chroms=None,
age=None,
col=(0, 0, 1)):
"""Draw a mark on a branch of an ARG"""
if node is None:
node = arglib.split_to_arg_branch(arg, pos, chroms)
if parent is None:
assert pos is not None
parent = arg.get_local_parent(node, pos)
if node and parent:
if age is None:
t = random.uniform(layout[node][1], layout[parent][1])
else:
t = layout[node][1] + (age - node.age)
nx, ny = layout[node]
return draw_mark(nx, t, col=col)
else:
return group()
def draw_branch(arg, layout, node=None, parent=None, chroms=None,
pos=None, col=None):
"""Draw a mark on a branch of an ARG"""
if node is None:
node = arglib.split_to_arg_branch(arg, pos, chroms)
if parent is None:
assert pos is not None
parent = arg.get_local_parent(node, pos)
if node and parent:
x1, y1, x2, y2 = get_branch_layout(layout, node, parent)
if col is None:
return lines(x1, y1, x2, y2)
else:
return lines(color(*col), x1, y1, x2, y2)
else:
return group()
def draw_branch_mark(arg, layout, node=None, parent=None, pos=None,
chroms=None, age=None, col=(0,0,1)):
"""Draw a mark on a branch of an ARG"""
if node is None:
node = arglib.split_to_arg_branch(arg, pos, chroms)
if parent is None:
assert pos is not None
parent = arg.get_local_parent(node, pos)
if node and parent:
if age is None:
t = random.uniform(layout[node][1], layout[parent][1])
else:
t = layout[node][1] + (age - node.age)
nx, ny = layout[node]
return draw_mark(nx, t, col=col)
else:
return group()
def draw_branch(arg, layout, node=None, parent=None, chroms=None,
pos=None, col=None):
"""Draw a mark on a branch of an ARG"""
if node is None:
node = arglib.split_to_arg_branch(arg, pos, chroms)
if parent is None:
assert pos is not None
parent = arg.get_local_parent(node, pos)
if node and parent:
x1, y1, x2, y2 = get_branch_layout(layout, node, parent)
if col is None:
return lines(x1, y1, x2, y2)
else:
return lines(color(*col), x1, y1, x2, y2)
else:
return group()
def draw_arg_threads(arg, blocks, layout, sites=None,
chrom_colors=None, chrom_color=[.2,.2,.8,.8],
snp_colors={"compat": [1, 0, 0],
"noncompat": [0, 1, 0]},
spr_alpha=1,
spr_trim=10,
compat=False,
draw_group=None,
win=None):
leaf_names = set(arg.leaf_names())
# TEST:
rnodes = dict((r.pos, r) for r in arg if r.event == "recomb")
if draw_group is None:
draw_group = group()
# set chromosome color
if chrom_colors is None:
chrom_colors = {}
for name in leaf_names:
chrom_colors[name] = chrom_color
spr_colors = {}
for name in leaf_names:
spr_colors[name] = list(chrom_colors[name])
if len(spr_colors[name]) < 4:
spr_colors[name].append(1.0)
spr_colors[name][3] *= spr_alpha
trims = []
for k, (x1, x2) in enumerate(blocks):
# calc trims
length = x2 - x1
minlen = 0
spr_trim2 = min(spr_trim, (length - minlen) / 2.0)
trims.append((x1 + spr_trim2, x2 - spr_trim2))
trim = trims[-1]
# horizontal lines
l = []
for name in leaf_names:
c = chrom_colors[name]
y = layout[k][name]
l.extend([color(*c), trim[0], y, trim[1], y])
draw_group.append(lines(*l))
# SPRs
if k > 0:
l = []
# TEST:
#rnode = rnodes.get(x1, None)
#young = (rnode is not None and rnode.age < 500)
for name in leaf_names:
#c = [1,0,0] if young else spr_colors[name]
c = spr_colors[name]
y1 = layout[k-1][name]
y2 = layout[k][name]
l.extend([color(*c), trims[k-1][1], y1, trims[k][0], y2])
draw_group.append(lines(*l))
# hotspots
g = group()
for name in leaf_names:
y = layout[k][name]
g.append(hotspot("click", x1+spr_trim, y+.4, x2-spr_trim, y-.4,
chrom_click(win, name, (x1, x2))))
draw_group.append(g)
# SNPs
tree = None
if sites:
l = []
for pos, col in sites.iter_region(x1, x2):
split = set(sites.get_minor(pos)) & leaf_names
if len(split) == 0:
continue
if compat:
if tree is None:
tree = arg.get_marginal_tree((x1+x2)/2.0)
arglib.remove_single_lineages(tree)
node = arglib.split_to_arg_branch(tree, pos-.5, split)
if node is not None:
derived = list(tree.leaf_names(node))
c = color(*snp_colors["compat"])
else:
c = color(*snp_colors["noncompat"])
derived = split
else:
c = color(*snp_colors["compat"])
derived = split
for d in derived:
if d in layout[k]:
y = layout[k][d]
l.extend([c, pos, y+.4, pos, y-.4])
draw_group.append(lines(*l))
return draw_group
def draw_arg_threads(arg,
blocks,
layout,
sites=None,
chrom_colors=None,
chrom_color=[.2, .2, .8, .8],
snp_colors={
"compat": [1, 0, 0],
"noncompat": [0, 1, 0]
},
get_snp_color=None,
spr_alpha=1,
spr_trim=10,
compat=False,
draw_group=None,
win=None):
leaf_names = set(arg.leaf_names())
# TEST:
rnodes = dict((r.pos, r) for r in arg if r.event == "recomb")
if draw_group is None:
draw_group = group()
# set chromosome color
if chrom_colors is None:
chrom_colors = {}
for name in leaf_names:
chrom_colors[name] = chrom_color
spr_colors = {}
for name in leaf_names:
spr_colors[name] = list(chrom_colors[name])
if len(spr_colors[name]) < 4:
spr_colors[name].append(1.0)
spr_colors[name][3] *= spr_alpha
trims = []
for k, (x1, x2) in enumerate(blocks):
# calc trims
length = x2 - x1
minlen = 0
spr_trim2 = min(spr_trim, (length - minlen) / 2.0)
trims.append((x1 + spr_trim2, x2 - spr_trim2))
trim = trims[-1]
# horizontal lines
l = []
for name in leaf_names:
c = chrom_colors[name]
y = layout[k][name]
l.extend([color(*c), trim[0], y, trim[1], y])
draw_group.append(lines(*l))
# SPRs
if k > 0:
l = []
# TEST:
#rnode = rnodes.get(x1, None)
#young = (rnode is not None and rnode.age < 500)
for name in leaf_names:
#c = [1,0,0] if young else spr_colors[name]
c = spr_colors[name]
y1 = layout[k - 1][name]
y2 = layout[k][name]
l.extend([color(*c), trims[k - 1][1], y1, trims[k][0], y2])
draw_group.append(lines(*l))
# hotspots
g = group()
for name in leaf_names:
y = layout[k][name]
g.append(
hotspot("click", x1 + spr_trim, y + .4, x2 - spr_trim, y - .4,
chrom_click(win, name, (x1, x2))))
draw_group.append(g)
# SNPs
tree = None
if sites:
l = []
for pos, col in sites.iter_region(x1, x2):
split = set(sites.get_minor(pos)) & leaf_names
if len(split) == 0:
continue
if compat:
if tree is None:
tree = arg.get_marginal_tree((x1 + x2) / 2.0)
arglib.remove_single_lineages(tree)
node = arglib.split_to_arg_branch(tree, pos - .5, split)
if node is not None:
derived = list(tree.leaf_names(node))
c = color(*snp_colors["compat"])
else:
c = color(*snp_colors["noncompat"])
derived = split
else:
c = color(*snp_colors["compat"])
derived = split
if get_snp_color and derived:
allele = sites.get(pos, next(iter(derived)))
c = color(*get_snp_color(arg.chrom, pos, allele))
for d in derived:
if d in layout[k]:
y = layout[k][d]
l.extend([c, pos, y + .4, pos, y - .4])
draw_group.append(lines(*l))
return draw_group