def ultrametricize(node):
import layout
n2c = layout.calc_node_positions(node, 1.0, 1.0, scaled=False)
for n in node.descendants():
c = n2c[n]
n.length = c.x - n2c[n.parent].x
def style_nodes(root, request, selected_node_id=None, wscale=1.0, scaled=True):
bgcolor = "black"
selcolor = "red"
leaves = root.leaves()
l2d = root.leaf_distances(measure=phylo.INTERNODES)[root.id]
height = len(leaves) * 3
unit = 3.0
width = max([l2d[lf.id] for lf in leaves]) * unit * wscale
width = min(width, 65)
rpad = max([len(lf.label or "") for lf in leaves]) * 0.7
lpad = max(1, len(root.label or []) * 0.7)
width += rpad + 2 + lpad
branchwidth = 0.75
n2c = layout.calc_node_positions(root,
width,
height,
lpad=lpad + 1,
tpad=1,
bpad=2.5,
rpad=rpad + 1,
scaled=scaled)
n2c[root].px = 1
for node in root.iternodes():
coords = n2c[node]
w = coords.x - coords.px
node.hbranch_style["width"] = w
node.hbranch_style["height"] = branchwidth
node.hbranch_style["top"] = coords.y + 0.5
node.hbranch_style["left"] = coords.px
node.hbranch_style["background-color"] = bgcolor
if coords.py is None:
coords.py = coords.y
if coords.py < coords.y:
h = coords.y - coords.py
y = coords.py
else:
h = coords.py - coords.y
y = coords.y
node.vbranch_style["width"] = 0.5 * branchwidth
node.vbranch_style["height"] = h
node.vbranch_style["top"] = y + 0.5
node.vbranch_style["left"] = coords.px
node.vbranch_style["background-color"] = bgcolor
if node.istip:
node.label_style["top"] = coords.y - 0.5
node.label_style["left"] = coords.x + 0.25
node.label_style["width"] = len(node.label or "")
node.label_style["text-align"] = "left"
else:
node.label_style["text-align"] = "right"
node.label_style["width"] = len(node.label or "")
node.label_style["top"] = coords.y - 0.5
node.label_style["left"] = coords.x - len(node.label or "")
node.ref_style["top"] = coords.y - 0.5
node.ref_style["left"] = coords.x + 0.25
if selected_node_id:
for n in root.iternodes():
if n.id == selected_node_id:
for m in n.iternodes():
m.vbranch_style["background-color"] = selcolor
m.hbranch_style["background-color"] = selcolor
break
return width, height
def style_nodes(root, collapsed=None, selected_node_id=None, wscale=1.0):
style = defaultdict(Storage)
collapsed = collapsed or set()
bgcolor = "gray"
selcolor = "red"
leaves = getleaves(root, collapsed=collapsed)
l2d = leaf_distances(root, collapsed=collapsed)
height = len(leaves) * 2.5
unit = 3.0
width = max([l2d[lf] for lf in leaves]) * unit * wscale
width = min(width, 65)
rpad = max([len(lf.label or "") for lf in leaves]) * 0.7
lpad = max(1, len(root.label or []) * 0.7)
width += rpad + 2 + lpad
branchwidth = 0.75
n2c = layout.calc_node_positions(
root, width, height, lpad=lpad + 1, tpad=1, bpad=2.5, rpad=rpad + 1, collapsed=collapsed, scaled=False
)
n2c[root].px = 1
for node in root.iternodes(f=lambda x: x.rec.id not in collapsed):
coords = n2c[node]
style[node].x = coords.x
style[node].y = coords.y
w = coords.x - coords.px
pos = "absolute"
style[node].hbranch = Storage()
hbranch = style[node].hbranch
hbranch["position"] = pos
hbranch["width"] = w
hbranch["height"] = branchwidth
hbranch["top"] = coords.y + 0.5
hbranch["left"] = coords.px
hbranch["background-color"] = bgcolor
if float(node.rec.bootstrap_support or 0) > 0.70:
hbranch["background-color"] = "green"
if coords.py is None:
coords.py = coords.y
if coords.py < coords.y:
h = coords.y - coords.py
y = coords.py
else:
h = coords.py - coords.y
y = coords.y
style[node].vbranch = Storage()
vbranch = style[node].vbranch
vbranch["position"] = pos
vbranch["width"] = 0.5 * branchwidth
vbranch["height"] = h
vbranch["top"] = y + 0.5
vbranch["left"] = coords.px
vbranch["background-color"] = bgcolor
style[node].label = Storage()
label = style[node].label
label["position"] = pos
if node.isleaf or node.rec.id in collapsed:
label["top"] = coords.y - 0.75
label["left"] = coords.x + 0.25
if node.rec.otu and node.rec.otu.taxon:
s = node.rec.otu.taxon.name
label["width"] = len(s)
else:
label["width"] = len(node.label or "")
label["text-align"] = "left"
else:
label["text-align"] = "right"
label["width"] = len(node.label or "")
label["top"] = coords.y - 0.75
label["left"] = coords.x - len(str(node.label or ""))
style[node].ref = Storage()
ref = style[node].ref
ref["position"] = pos
ref["top"] = coords.y - 0.5
ref["left"] = coords.x + 0.25
if selected_node_id:
for n in root.iternodes(f=lambda x: x.rec.id not in collapsed):
if n.rec.id == selected_node_id:
for m in n.iternodes():
style[m].vbranch["background-color"] = selcolor
style[m].hbranch["background-color"] = selcolor
break
return width, height, style
def style_nodes(root, collapsed=None, selected_node_id=None, wscale=1.0):
style = defaultdict(Storage)
collapsed = collapsed or set()
bgcolor = "gray"
selcolor = "red"
leaves = getleaves(root, collapsed=collapsed)
l2d = leaf_distances(root, collapsed=collapsed)
height = len(leaves) * 2.5
unit = 3.0
width = max([l2d[lf] for lf in leaves]) * unit * wscale
width = min(width, 65)
rpad = max([len(lf.label or "") for lf in leaves]) * 0.7
lpad = max(1, len(root.label or []) * 0.7)
width += rpad + 2 + lpad
branchwidth = 0.75
n2c = layout.calc_node_positions(root,
width,
height,
lpad=lpad + 1,
tpad=1,
bpad=2.5,
rpad=rpad + 1,
collapsed=collapsed,
scaled=False)
n2c[root].px = 1
for node in root.iternodes(f=lambda x: x.rec.id not in collapsed):
coords = n2c[node]
style[node].x = coords.x
style[node].y = coords.y
w = coords.x - coords.px
pos = "absolute"
style[node].hbranch = Storage()
hbranch = style[node].hbranch
hbranch["position"] = pos
hbranch["width"] = w
hbranch["height"] = branchwidth
hbranch["top"] = coords.y + 0.5
hbranch["left"] = coords.px
hbranch["background-color"] = bgcolor
if float(node.rec.bootstrap_support or 0) > 0.70:
hbranch["background-color"] = "green"
if coords.py is None:
coords.py = coords.y
if coords.py < coords.y:
h = coords.y - coords.py
y = coords.py
else:
h = coords.py - coords.y
y = coords.y
style[node].vbranch = Storage()
vbranch = style[node].vbranch
vbranch["position"] = pos
vbranch["width"] = 0.5 * branchwidth
vbranch["height"] = h
vbranch["top"] = y + 0.5
vbranch["left"] = coords.px
vbranch["background-color"] = bgcolor
style[node].label = Storage()
label = style[node].label
label["position"] = pos
if node.isleaf or node.rec.id in collapsed:
label["top"] = coords.y - 0.75
label["left"] = coords.x + 0.25
if node.rec.otu and node.rec.otu.taxon:
s = node.rec.otu.taxon.name
label["width"] = len(s)
else:
label["width"] = len(node.label or "")
label["text-align"] = "left"
else:
label["text-align"] = "right"
label["width"] = len(node.label or "")
label["top"] = coords.y - 0.75
label["left"] = coords.x - len(str(node.label or ""))
style[node].ref = Storage()
ref = style[node].ref
ref["position"] = pos
ref["top"] = coords.y - 0.5
ref["left"] = coords.x + 0.25
if selected_node_id:
for n in root.iternodes(f=lambda x: x.rec.id not in collapsed):
if n.rec.id == selected_node_id:
for m in n.iternodes():
style[m].vbranch["background-color"] = selcolor
style[m].hbranch["background-color"] = selcolor
break
return width, height, style
svg = fig.SVG()
vb = "%s %s %s %s" % (0, 0, w, h)
svgfig.canvas(svg, width=w, height=h, viewBox=vb).save(fname)
#svg.save(fname)
width = float(commands.getoutput("inkscape -W '%s'" % fname))
height = float(commands.getoutput("inkscape -H '%s'" % fname))
os.remove(fname)
return width, height
w = 400.0
h = 800.0
r = newick.parse(file("test.newick").read())
r.order_subtrees_by_size()
n2c = layout.calc_node_positions(r, w, h, scaled=True)
ntips = float(len(r.leaves()))
fontsize = h / ntips
## bbox = svgfig.Rect(1,1,w-1,h-1)
branches = []
labels = []
for n, c in n2c.items():
if n.parent:
pc = n2c[n.parent]
d = ((c.x, c.y), (pc.x, c.y), (pc.x, pc.y))
line = svgfig.Poly(d)
branches.append(line)
if n.label:
fname = tempfile.mktemp(suffix=".svg")
svg = fig.SVG()
vb = "%s %s %s %s" % (0, 0, w, h)
svgfig.canvas(svg, width=w, height=h, viewBox=vb).save(fname)
#svg.save(fname)
width = float(commands.getoutput("inkscape -W '%s'" % fname))
height = float(commands.getoutput("inkscape -H '%s'" % fname))
os.remove(fname)
return width, height
w = 400.0
h = 800.0
r = newick.parse(file("test.newick").read())
r.order_subtrees_by_size()
n2c = layout.calc_node_positions(r, w, h, scaled=True)
ntips = float(len(r.leaves()))
fontsize = h/ntips
## bbox = svgfig.Rect(1,1,w-1,h-1)
branches = []
labels = []
for n, c in n2c.items():
if n.parent:
pc = n2c[n.parent]
d = ((c.x, c.y), (pc.x, c.y), (pc.x, pc.y))
line = svgfig.Poly(d)
branches.append(line)
if n.label:
def style_nodes(root, request, selected_node_id=None, wscale=1.0, scaled=True):
bgcolor = "black"
selcolor = "red"
leaves = root.leaves()
l2d = root.leaf_distances(measure=phylo.INTERNODES)[root.id]
height = len(leaves)*3
unit = 3.0
width = max([ l2d[lf.id] for lf in leaves ]) * unit * wscale
width = min(width, 65)
rpad = max([ len(lf.label or "") for lf in leaves ]) * 0.7
lpad = max(1, len(root.label or []) * 0.7)
width += rpad+2 + lpad
branchwidth = 0.75
n2c = layout.calc_node_positions(
root, width, height,
lpad=lpad+1, tpad=1, bpad=2.5, rpad=rpad+1,
scaled=scaled
)
n2c[root].px = 1
for node in root.iternodes():
coords = n2c[node]
w = coords.x-coords.px
node.hbranch_style["width"] = w
node.hbranch_style["height"] = branchwidth
node.hbranch_style["top"] = coords.y+0.5
node.hbranch_style["left"] = coords.px
node.hbranch_style["background-color"] = bgcolor
if coords.py is None:
coords.py = coords.y
if coords.py < coords.y:
h = coords.y-coords.py
y = coords.py
else:
h = coords.py-coords.y
y = coords.y
node.vbranch_style["width"] = 0.5 * branchwidth
node.vbranch_style["height"] = h
node.vbranch_style["top"] = y+0.5
node.vbranch_style["left"] = coords.px
node.vbranch_style["background-color"] = bgcolor
if node.istip:
node.label_style["top"] = coords.y-0.5
node.label_style["left"] = coords.x+0.25
node.label_style["width"] = len(node.label or "")
node.label_style["text-align"] = "left"
else:
node.label_style["text-align"] = "right"
node.label_style["width"] = len(node.label or "")
node.label_style["top"] = coords.y-0.5
node.label_style["left"] = coords.x-len(node.label or "")
node.ref_style["top"] = coords.y-0.5
node.ref_style["left"] = coords.x+0.25
if selected_node_id:
for n in root.iternodes():
if n.id == selected_node_id:
for m in n.iternodes():
m.vbranch_style["background-color"] = selcolor
m.hbranch_style["background-color"] = selcolor
break
return width, height
def ultrametricize(node):
import layout
n2c = layout.calc_node_positions(node, 1.0, 1.0, scaled=False)
for n in node.descendants():
c = n2c[n]
n.length = c.x - n2c[n.parent].x
