def setup_recon(self, recon=None):
# construct default reconciliation
if recon == None and self.stree and self.gene2species:
self.recon = phylo.reconcile(self.tree, self.stree, self.gene2species)
else:
self.recon = recon
# construct events
if self.recon:
self.events = phylo.label_events(self.tree, self.recon)
self.losses = phylo.find_loss(self.tree, self.stree, self.recon)
else:
self.events = None
self.losses = None
def draw_tree(tree,
labels={},
xscale=100,
yscale=20,
canvas=None,
leafPadding=10,
leafFunc=lambda x: str(x.name),
labelOffset=None,
fontSize=10,
labelSize=None,
minlen=1,
maxlen=util.INF,
filename=sys.stdout,
rmargin=150,
lmargin=10,
tmargin=0,
bmargin=None,
colormap=None,
stree=None,
layout=None,
gene2species=None,
lossColor=(0, 0, 1),
dupColor=(1, 0, 0),
eventSize=4,
legendScale=False,
autoclose=None,
extendRoot=True,
labelLeaves=True,
drawHoriz=True,
nodeSize=0):
# set defaults
fontRatio = 8. / 11.
if labelSize == None:
labelSize = .7 * fontSize
if labelOffset == None:
labelOffset = -1
if bmargin == None:
bmargin = yscale
if sum(x.dist for x in tree.nodes.values()) == 0:
legendScale = False
minlen = xscale
if colormap == None:
for node in tree:
node.color = (0, 0, 0)
else:
colormap(tree)
if stree and gene2species:
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
losses = phylo.find_loss(tree, stree, recon)
else:
events = None
losses = None
if len(labels) > 0 or (stree and gene2species):
drawHoriz = True
# layout tree
if layout is None:
coords = treelib.layout_tree(tree, xscale, yscale, minlen, maxlen)
else:
coords = layout
xcoords, ycoords = zip(*coords.values())
maxwidth = max(xcoords)
maxheight = max(ycoords) + labelOffset
# initialize canvas
if canvas == None:
canvas = svg.Svg(util.open_stream(filename, "w"))
width = int(rmargin + maxwidth + lmargin)
height = int(tmargin + maxheight + bmargin)
canvas.beginSvg(width, height)
if autoclose == None:
autoclose = True
else:
if autoclose == None:
autoclose = False
# draw tree
def walk(node):
x, y = coords[node]
if node.parent:
parentx, parenty = coords[node.parent]
else:
if extendRoot:
parentx, parenty = 0, y
else:
parentx, parenty = x, y # e.g. no branch
# draw branch
if drawHoriz:
canvas.line(parentx, y, x, y, color=node.color)
else:
canvas.line(parentx, parenty, x, y, color=node.color)
# draw branch labels
if node.name in labels:
branchlen = x - parentx
lines = str(labels[node.name]).split("\n")
labelwidth = max(map(len, lines))
labellen = min(labelwidth * fontRatio * fontSize,
max(int(branchlen - 1), 0))
for i, line in enumerate(lines):
canvas.text(
line, parentx + (branchlen - labellen) / 2.,
y + labelOffset + (-len(lines) + 1 + i) * (labelSize + 1),
labelSize)
# draw nodes
if nodeSize > 0:
canvas.circle(x,
y,
nodeSize,
strokeColor=svg.null,
fillColor=node.color)
# draw leaf labels or recur
if node.is_leaf():
if labelLeaves:
canvas.text(leafFunc(node),
x + leafPadding,
y + fontSize / 2.,
fontSize,
fillColor=node.color)
else:
if drawHoriz:
# draw vertical part of branch
top = coords[node.children[0]][1]
bot = coords[node.children[-1]][1]
canvas.line(x, top, x, bot, color=node.color)
# draw children
for child in node.children:
walk(child)
canvas.beginTransform(("translate", lmargin, tmargin))
walk(tree.root)
if stree and gene2species:
draw_events(canvas,
tree,
coords,
events,
losses,
lossColor=lossColor,
dupColor=dupColor,
size=eventSize)
canvas.endTransform()
# draw legend
if legendScale:
if legendScale == True:
# automatically choose a scale
length = maxwidth / float(xscale)
order = math.floor(math.log10(length))
length = 10**order
drawScale(lmargin,
tmargin + maxheight + bmargin - fontSize,
length,
xscale,
fontSize,
canvas=canvas)
if autoclose:
canvas.endSvg()
return canvas
def draw_tree(tree, labels={}, xscale=100, yscale=20, canvas=None,
leafPadding=10, leafFunc=lambda x: str(x.name),
labelOffset=None, fontSize=10, labelSize=None,
minlen=1, maxlen=util.INF, filename=sys.stdout,
rmargin=150, lmargin=10, tmargin=0, bmargin=None,
colormap=None,
stree=None,
layout=None,
gene2species=None,
lossColor=(0, 0, 1),
dupColor=(1, 0, 0),
eventSize=4,
legendScale=False, autoclose=None,
extendRoot=True, labelLeaves=True, drawHoriz=True, nodeSize=0):
# set defaults
fontRatio = 8. / 11.
if labelSize == None:
labelSize = .7 * fontSize
if labelOffset == None:
labelOffset = -1
if bmargin == None:
bmargin = yscale
if sum(x.dist for x in tree.nodes.values()) == 0:
legendScale = False
minlen = xscale
if colormap == None:
for node in tree:
node.color = (0, 0, 0)
else:
colormap(tree)
if stree and gene2species:
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
losses = phylo.find_loss(tree, stree, recon)
else:
events = None
losses = None
if len(labels) > 0 or (stree and gene2species):
drawHoriz = True
# layout tree
if layout is None:
coords = treelib.layout_tree(tree, xscale, yscale, minlen, maxlen)
else:
coords = layout
xcoords, ycoords = zip(* coords.values())
maxwidth = max(xcoords)
maxheight = max(ycoords) + labelOffset
# initialize canvas
if canvas == None:
canvas = svg.Svg(util.open_stream(filename, "w"))
width = int(rmargin + maxwidth + lmargin)
height = int(tmargin + maxheight + bmargin)
canvas.beginSvg(width, height)
if autoclose == None:
autoclose = True
else:
if autoclose == None:
autoclose = False
# draw tree
def walk(node):
x, y = coords[node]
if node.parent:
parentx, parenty = coords[node.parent]
else:
if extendRoot:
parentx, parenty = 0, y
else:
parentx, parenty = x, y # e.g. no branch
# draw branch
if drawHoriz:
canvas.line(parentx, y, x, y, color=node.color)
else:
canvas.line(parentx, parenty, x, y, color=node.color)
# draw branch labels
if node.name in labels:
branchlen = x - parentx
lines = str(labels[node.name]).split("\n")
labelwidth = max(map(len, lines))
labellen = min(labelwidth * fontRatio * fontSize,
max(int(branchlen-1), 0))
for i, line in enumerate(lines):
canvas.text(line,
parentx + (branchlen - labellen)/2.,
y + labelOffset
+(-len(lines)+1+i)*(labelSize+1),
labelSize)
# draw nodes
if nodeSize > 0:
canvas.circle(x, y, nodeSize, strokeColor=svg.null, fillColor=node.color)
# draw leaf labels or recur
if node.is_leaf():
if labelLeaves:
canvas.text(leafFunc(node),
x + leafPadding, y+fontSize/2., fontSize,
fillColor=node.color)
else:
if drawHoriz:
# draw vertical part of branch
top = coords[node.children[0]][1]
bot = coords[node.children[-1]][1]
canvas.line(x, top, x, bot, color=node.color)
# draw children
for child in node.children:
walk(child)
canvas.beginTransform(("translate", lmargin, tmargin))
walk(tree.root)
if stree and gene2species:
draw_events(canvas, tree, coords, events, losses,
lossColor=lossColor,
dupColor=dupColor,
size=eventSize)
canvas.endTransform()
# draw legend
if legendScale:
if legendScale == True:
# automatically choose a scale
length = maxwidth / float(xscale)
order = math.floor(math.log10(length))
length = 10 ** order
drawScale(lmargin, tmargin + maxheight + bmargin - fontSize,
length, xscale, fontSize, canvas=canvas)
if autoclose:
canvas.endSvg()
return canvas