def make_color_legend(filename,
colormap,
start,
end,
step,
width=100,
height=10,
display=False):
from rasmus import util
if filename is None:
filename = util.tempfile(".", "colormap", ".svg")
temp = True
else:
temp = False
s = svg.Svg(util.open_stream(filename, "w"))
s.beginSvg(width, height)
xscale = float(width) / (end + step - start)
for i in util.frange(start, end + step, step):
color = colormap.get(i)
s.rect((i - start) * xscale, 0, step * xscale, height, color, color)
s.endSvg()
s.close()
# display
if display:
os.system("display %s" % filename)
# clean up temp files
if temp:
os.remove(filename)
def drawDistRuler(names,
dists,
scale=500,
padding=10,
textsize=12,
notchsize=2,
labelpadding=5,
distsize=9,
filename=sys.stdout):
"""Produce a ruler of pairwise distances"""
nameswidth = textsize * max(map(len, names))
out = svg.Svg(util.open_stream(filename, "w"))
out.beginSvg(scale * max(dists) + 2 * padding,
2 * padding + nameswidth + 5 * distsize)
out.beginTransform(("translate", padding, nameswidth + padding))
# draw ruler
out.line(0, 0, scale * max(dists), 0)
for name, dist in zip(names, dists):
x = scale * dist
out.text(name, x + textsize / 2.0, -labelpadding, textsize, angle=-90)
out.line(x, notchsize, x, -notchsize)
out.text("%.3f" % dist,
x + textsize / 2.0,
labelpadding + distsize * 3.5,
distsize,
angle=-90)
out.endTransform()
out.endSvg()
def make_color_legend(filename, colormap, start, end, step,
width=100, height=10):
from rasmus import util
s = svg.Svg(util.open_stream(filename, "w"))
s.beginSvg(width, height)
xscale = float(width) / (end + step - start)
for i in util.frange(start, end + step, step):
color = colormap.get(i)
s.rect((i-start) * xscale,
0,
step*xscale, height,
color, color)
s.endSvg()
def draw_tree(tree,
brecon,
stree,
xscale=100,
yscale=100,
leaf_padding=10,
label_size=None,
label_offset=None,
font_size=12,
stree_font_size=20,
canvas=None,
autoclose=True,
rmargin=10,
lmargin=100,
tmargin=100,
bmargin=100,
tree_color=(0, 0, 0),
tree_trans_color=(0, 0, 0),
stree_color=(.3, .7, .3),
snode_color=(.2, .2, .7),
loss_color=(1, 1, 1),
loss_color_border=(.5, .5, .5),
dup_color=(0, 0, 1),
dup_color_border=(0, 0, 1),
trans_color=(1, 1, 0),
trans_color_border=(.5, .5, 0),
gtrans_color=(1, 0, 0),
gtrans_color_border=(.5, 0, 0),
event_size=10,
snames=None,
rootlen=None,
stree_width=.8,
filename="tree.svg"):
'''Takes as input a parasite tree, tree, a reconciliation file, brecon, a host tree, stree, as well as
sizes and colors of the trees components and returns a drawing of the reconciliation of the parasite
tree on the host tree with event nodes of specified colors'''
# set defaults
font_ratio = 8. / 11.
if label_size is None:
label_size = .7 * font_size
if sum(x.dist for x in tree.nodes.values()) == 0:
legend_scale = False
minlen = xscale
if snames is None:
snames = dict((x, x) for x in stree.leaf_names())
# layout stree
slayout = treelib1.layout_tree(stree, xscale, yscale)
if rootlen is None:
rootlen = .1 * max(l[0] for l in slayout.values())
# setup slayout
x, y = slayout[stree.root]
slayout[None] = (x - rootlen, y)
for node, (x, y) in slayout.items():
slayout[node] = (x + rootlen, y - .5 * yscale)
# layout tree
ylists = defaultdict(lambda: [])
yorders = {}
# layout speciations and genes (y)
for node in tree.preorder():
if node == list(tree.preorder())[0]:
rootNode = node.name
yorders[node] = []
for ev in brecon[node]:
snode, event, frequency = ev
if event == "spec" or event == "gene" or event == "loss":
yorders[node].append(len(ylists[snode]))
ylists[snode].append(node)
# layout dups and transfers (y)
for node in tree.postorder():
for ev in brecon[node]:
snode, event, frequency = ev
if event != "spec" and event != "gene" and event != "loss":
# Find number of nodes on a single branch for y-coord
v = [
yorders[child] for child in node.children
if brecon[child][-1][0] == snode
]
if len(v) == 0:
yorders[node].append(0)
else:
yorders[node].append(stats.mean(flatten(v)))
# layout node (x)
xorders = {
} #Dictionary to record number of nodes on a single branch for x-coord
branchFrac = {} #Dictionary to record the placement of a node on a branch
for node in tree.postorder():
for n in range(len(brecon[node])):
snode, event, frequency = brecon[node][n]
if event == "spec" or event == "gene" or event == "loss":
# Speciation, gene, and loss events happen at host vertices
if not node in branchFrac:
branchFrac[node] = 0
else: # Transfers and duplications occur on branches
v = [branchFrac[child] for child in node.children]
if len(v) == 0:
branchFrac[node] = 1
else:
branchFrac[node] = max(v) + 1
for node in tree.preorder():
xorders[node] = []
for n in range(len(brecon[node])):
snode, event, frequency = brecon[node][n]
if event == "spec" or event == "gene" or event == "loss":
# Speciation, gene, and loss events happen on vertices, not branches
xorders[node].append(0)
else:
if node.parent and containsTransOrDup(node.parent, brecon):
# set branchFrac to the branch Frac of the parent, they are
# on the same branch
branchFrac[node] = branchFrac[node.parent]
if containsLoss(node, brecon):
# if following a loss, first transfer/duplication event on branch
xorders[node].append(1)
elif not node.parent: # Root of tree
xorders[node].append(0)
else:
xorders[node].append(maxList(xorders[node.parent]) + 1)
# setup layout
layout = {None: [slayout[brecon[tree.root][-1][0].parent]]}
for node in tree.preorder():
for n in range(len(brecon[node])):
snode, event, frequency = brecon[node][n]
nx, ny = slayout[snode]
px, py = slayout[snode.parent]
(npx, npy) = layout[node.parent][-1]
# set spacing between nodes on the same branch
frac = 50
while branchFrac[node] * frac >= nx - px:
frac = frac - 5
# calc x
if event == "trans" or event == "gtrans":
if npx > px: # transfer parent is farther forward in time than host parent
x = npx + frac
else:
x = px + frac
elif event == "dup":
x = px + frac
else:
x = nx
# calc y
deltay = ny - py
slope = deltay / float(nx - px)
deltax2 = x - px
deltay2 = slope * deltax2
offset = py + deltay2
frac = (yorders[node][n] +
1) / float(max(len(ylists[snode]), 1) + 1)
y = offset + (frac - .5) * stree_width * yscale
if node in layout: layout[node].append((x, y))
else:
layout[node] = [(x, y)]
# order brecon nodes temporally
brecon[node] = orderLoss(node, brecon, layout)
# order layout nodes temporally
layout[node] = orderLayout(node, layout)
if y > max(l[1] for l in slayout.values()) + 50:
print nx, ny
print px, py
print offset, frac
print ylists[snode], yorders[node]
print brecon[node]
print node, snode, layout[node]
# layout label sizes
max_label_size = max(len(x.name)
for x in tree.leaves()) * font_ratio * font_size
max_slabel_size = max(
len(x.name) for x in stree.leaves()) * font_ratio * stree_font_size
'''
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
# layout tree
if layout is None:
coords = treelib.layout_tree(tree, xscale, yscale, minlen, maxlen)
else:
coords = layout
'''
xcoords, ycoords = zip(*slayout.values())
maxwidth = max(xcoords) + max_label_size + max_slabel_size
maxheight = max(ycoords) + yscale
# initialize canvas
if canvas is None:
canvas = svg.Svg(util.open_stream(filename, "w"))
width = int(rmargin + maxwidth + lmargin)
height = int(tmargin + maxheight + bmargin)
canvas.beginSvg(width, height)
canvas.beginStyle("font-family: \"Sans\";")
if autoclose == None:
autoclose = True
else:
if autoclose == None:
autoclose = False
canvas.beginTransform(("translate", lmargin, tmargin))
draw_stree(canvas,
stree,
slayout,
yscale=yscale,
stree_width=stree_width,
stree_color=stree_color,
snode_color=snode_color)
# draw stree leaves
for node in stree:
x, y = slayout[node]
if node.is_leaf():
canvas.text(snames[node.name],
x + leaf_padding + max_label_size,
y + stree_font_size / 2.,
stree_font_size,
fillColor=snode_color)
# draw tree
for node in tree:
containsL = containsLoss(node, brecon)
for n in range(len(brecon[node])):
x, y = layout[node][n]
if containsL == False: # no loss event
px, py = layout[node.parent][-1]
else: # loss event present
if n == 0: # event is loss
px, py = layout[node.parent][-1]
else: # event stems from loss
px, py = layout[node][n - 1]
trans = False
if node.parent:
snode, event, frequency = brecon[node][n]
if n == 0:
psnode, pevent, pfrequency = brecon[node.parent][-1]
# Event stemming from a loss event
else:
psnode, pevent, pfrequency = brecon[node][n - 1]
if pevent == "trans" or pevent == "gtrans":
if psnode != snode:
trans = True
else:
trans = False
if not trans:
canvas.line(x, y, px, py, color=tree_color)
# draw the transfer dashed line
else:
arch = 20
x2 = (x * .5 + px * .5) - arch
y2 = (y * .5 + py * .5)
x3 = (x * .5 + px * .5) - arch
y3 = (y * .5 + py * .5)
# draw regular transfer dashed line
if pevent == "trans":
canvas.write(
"<path d='M%f %f C%f %f %f %f %f %f' %s />\n " %
(x, y, x2, y2, x3, y3, px, py,
" style='stroke-dasharray: 4, 2' " +
svg.colorFields(tree_trans_color, (0, 0, 0, 0))))
# draw guilty transfer dashed line
else:
canvas.write(
"<path d='M%f %f C%f %f %f %f %f %f' %s />\n " %
(x, y, x2, y2, x3, y3, px, py,
" style='stroke-dasharray: 4, 2' " +
svg.colorFields(gtrans_color, (0, 0, 0, 0))))
# draw events
for node in tree:
if node.name == rootNode:
x, y = layout[node][0]
canvas.polygon((x-20, y, x-50, y+30,x-50, y+15, x-90, y+15, x-90,\
y-15, x-50, y-15, x-50, y-30), strokeColor = (1,.7,.3), \
fillColor = (1,.7,.3))
canvas.text("Root Node", x-88, y+5, font_size+2,\
fillColor = (0,0,0))
for n in range(len(brecon[node])):
snode, event, frequency = brecon[node][n]
frequency = float(frequency)
x, y = layout[node][n]
o = event_size / 2.0
if event == "loss": # draw boxes, frequencies of loss events
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=loss_color,
strokeColor=loss_color_border)
canvas.text("{:.3f}".format(frequency) + node.name,
x - o,
y - o,
font_size + 2,
fillColor=loss_color)
if event == "spec": # draw boxes, frequencies of speciation events
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=(0, 0, 0),
strokeColor=(0, 0, 0))
canvas.text("{:.3f}".format(frequency) + node.name,
x - o,
y - o,
font_size + 2,
fillColor=(0, 0, 0))
if event == "dup": # draw boxes, frequencies of duplication events
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=dup_color,
strokeColor=dup_color_border)
canvas.text("{:.3f}".format(frequency) + node.name,
x - o,
y - o,
font_size + 2,
fillColor=dup_color)
elif event == "trans": # draw boxes, frequencies of transfer events
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=trans_color,
strokeColor=trans_color_border)
canvas.text("{:.3f}".format(frequency) + node.name,
x - o,
y - o,
font_size + 2,
fillColor=trans_color)
elif event == "gtrans": # draw boxes, frequencies of guilty transfer events
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=gtrans_color,
strokeColor=gtrans_color_border)
canvas.text("{:.3f}".format(frequency) + node.name,
x - o,
y - o,
font_size + 2,
fillColor=gtrans_color)
# draw tree leaves
for node in tree:
for n in range(len(brecon[node])):
x, y = layout[node][n]
if node.is_leaf() and brecon[node][n][1] == "gene":
canvas.text(node.name,
x + leaf_padding,
y + font_size / 2.,
font_size + 2,
fillColor=(0, 0, 0))
canvas.endTransform()
if autoclose:
canvas.endStyle()
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
def heatmap(matrix,
width=20,
height=20,
colormap=None,
filename=None,
rlabels=None,
clabels=None,
display=True,
xdir=1,
ydir=1,
xmargin=0,
ymargin=0,
labelPadding=2,
labelSpacing=4,
mincutoff=None,
maxcutoff=None,
showVals=False,
formatVals=str,
valColor=black,
clabelsAngle=270,
clabelsPadding=None,
rlabelsAngle=0,
rlabelsPadding=None,
colors=None,
strokeColors=None,
valAnchor="start",
close=True):
from rasmus import util
if display and (not close):
raise Exception("must close file if display is used")
# determine filename
if filename is None:
filename = util.tempfile(".", "heatmap", ".svg")
temp = True
else:
temp = False
# determine colormap
if colors is None:
if colormap is None:
colormap = rainbowColorMap(util.flatten(matrix))
# determine matrix size and orientation
nrows = len(matrix)
ncols = len(matrix[0])
if xdir == 1:
xstart = xmargin
ranchor = "end"
coffset = width
elif xdir == -1:
xstart = xmargin + ncols * width
ranchor = "start"
coffset = 0
else:
raise Exception("xdir must be 1 or -1")
if ydir == 1:
ystart = ymargin
roffset = height
canchor = "start"
elif ydir == -1:
ystart = ymargin + nrows * width
roffset = 0
canchor = "end"
else:
raise Exception("ydir must be 1 or -1")
# begin svg
infile = util.open_stream(filename, "w")
s = svg.Svg(infile)
s.beginSvg(ncols * width + 2 * xmargin, nrows * height + 2 * ymargin)
# draw matrix
for i in xrange(nrows):
for j in xrange(ncols):
if mincutoff and matrix[i][j] < mincutoff:
continue
if maxcutoff and matrix[i][j] > maxcutoff:
continue
if colors:
color = colors[i][j]
else:
color = colormap.get(matrix[i][j])
if strokeColors:
strokeColor = strokeColors[i][j]
else:
strokeColor = color
s.rect(xstart + xdir * j * width, ystart + ydir * i * height,
xdir * width, ydir * height, strokeColor, color)
# draw values
if showVals:
# find text size
fontwidth = 7 / 11.0
textsize = []
for i in xrange(nrows):
for j in xrange(ncols):
if mincutoff and matrix[i][j] < mincutoff:
continue
if maxcutoff and matrix[i][j] > maxcutoff:
continue
strval = formatVals(matrix[i][j])
if len(strval) > 0:
textsize.append(
min(height, width / (float(len(strval)) * fontwidth)))
textsize = min(textsize)
if valAnchor == "start":
xoffset = 0
elif valAnchor == "middle":
xoffset = 0.5
elif valAnchor == "end":
xoffset = 1
else:
raise Exception("anchor not supported: %s" % valAnchor)
yoffset = int(ydir == -1)
for i in xrange(nrows):
for j in xrange(ncols):
if mincutoff and matrix[i][j] < mincutoff:
continue
if maxcutoff and matrix[i][j] > maxcutoff:
continue
strval = formatVals(matrix[i][j])
s.text(strval,
xstart + xdir * (j + xoffset) * width,
ystart + ydir * (i + yoffset) * height + height / 2.0 +
textsize / 2.0,
textsize,
fillColor=valColor,
anchor=valAnchor)
# draw labels
if rlabels is not None:
assert len(rlabels) == nrows, \
"number of row labels does not equal number of rows"
if rlabelsPadding is None:
rlabelsPadding = labelPadding
for i in xrange(nrows):
x = xstart - xdir * rlabelsPadding
y = ystart + roffset + ydir * i * height - labelSpacing / 2.
s.text(rlabels[i],
x,
y,
height - labelSpacing,
anchor=ranchor,
angle=rlabelsAngle)
if clabels is not None:
assert len(clabels) == ncols, \
"number of col labels does not equal number of cols"
if clabelsPadding is None:
clabelsPadding = labelPadding
for j in xrange(ncols):
x = xstart + coffset + xdir * j * width - labelSpacing / 2.
y = ystart - ydir * clabelsPadding
s.text(clabels[j],
x,
y,
width - labelSpacing,
anchor=canchor,
angle=clabelsAngle)
# end svg
if close:
s.endSvg()
s.close()
# display matrix
if display:
#if temp:
os.system("display %s" % filename)
#else:
# os.spawnl(os.P_NOWAIT, "display", "display", filename)
# clean up temp files
if temp:
os.remove(filename)
return s
def draw_tree(tree,
brecon,
stree,
xscale=100,
yscale=100,
leaf_padding=10,
label_size=None,
label_offset=None,
font_size=12,
stree_font_size=20,
canvas=None,
autoclose=True,
rmargin=10,
lmargin=10,
tmargin=0,
bmargin=0,
tree_color=(0, 0, 0),
tree_trans_color=(0, 0, 0),
stree_color=(.6, .3, .8),
snode_color=(.2, .2, .7),
loss_color=(1, 1, 1),
loss_color_border=(.5, .5, .5),
dup_color=(1, 0, 0),
dup_color_border=(.5, 0, 0),
trans_color=(0, 1, 0),
trans_color_border=(0, .5, 0),
event_size=10,
snames=None,
rootlen=None,
stree_width=.8,
filename="tree.svg"):
# set defaults
font_ratio = 8. / 11.
if label_size is None:
label_size = .7 * font_size
#if label_offset is None:
# label_offset = -1
if sum(x.dist for x in tree.nodes.values()) == 0:
legend_scale = False
minlen = xscale
if snames is None:
snames = dict((x, x) for x in stree.leaf_names())
# layout stree
slayout = treelib1.layout_tree(stree, xscale, yscale)
if rootlen is None:
rootlen = .1 * max(l[0] for l in slayout.values())
# setup slayout
x, y = slayout[stree.root]
slayout[None] = (x - rootlen, y)
for node, (x, y) in slayout.items():
slayout[node] = (x + rootlen, y - .5 * yscale)
# layout tree
ylists = defaultdict(lambda: [])
yorders = {}
# layout speciations and genes (y)
for node in tree.preorder():
for ev in brecon[node]:
snode, event, frequency = ev
if event == "spec" or event == "gene" or event == "loss":
yorders[node] = len(ylists[snode])
ylists[snode].append(node)
# layout dups and transfers (y)
for node in tree.postorder():
for ev in brecon[node]:
snode, event, frequency = ev
if event != "spec" and event != "gene" and event != "loss":
v = [
yorders[child] for child in node.children
if brecon[child][-1][0] == snode
]
if len(v) == 0:
yorders[node] = 0
else:
yorders[node] = stats.mean(v)
# layout node (x)
xorders = {}
xmax = defaultdict(lambda: 0)
for node in tree.postorder():
for ev in brecon[node]:
snode, event, frequency = ev
if event == "spec" or event == "gene" or event == "loss":
xorders[node] = 0
else:
v = [
xorders[child] for child in node.children
if brecon[child][-1][0] == snode
]
if len(v) == 0:
xorders[node] = 1
else:
xorders[node] = max(v) + 1
xmax[snode] = max(xmax[snode], xorders[node])
# setup layout
layout = {None: [slayout[brecon[tree.root][-1][0].parent]]}
for node in tree:
for ev in brecon[node]:
snode, event, frequency = ev
nx, ny = slayout[snode]
px, py = slayout[snode.parent]
# calc x
frac = (xorders[node]) / float(xmax[snode] + 1)
deltax = nx - px
x = nx - frac * deltax
# calc y
deltay = ny - py
slope = deltay / float(deltax)
deltax2 = x - px
deltay2 = slope * deltax2
offset = py + deltay2
frac = (yorders[node] + 1) / float(max(len(ylists[snode]), 1) + 1)
y = offset + (frac - .5) * stree_width * yscale
if node in layout: layout[node].append((x, y))
else:
layout[node] = [(x, y)]
brecon[node] = orderLoss(node, brecon, layout)
print "Brecon = ", brecon[node]
layout[node] = orderLayout(node, layout)
print "Layout = ", layout[node]
if y > max(l[1] for l in slayout.values()) + 50:
print nx, ny
print px, py
print offset, frac
print ylists[snode], yorders[node]
print brecon[node]
print node, snode, layout[node]
# layout label sizes
max_label_size = max(len(x.name)
for x in tree.leaves()) * font_ratio * font_size
max_slabel_size = max(
len(x.name) for x in stree.leaves()) * font_ratio * stree_font_size
'''
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
# layout tree
if layout is None:
coords = treelib.layout_tree(tree, xscale, yscale, minlen, maxlen)
else:
coords = layout
'''
xcoords, ycoords = zip(*slayout.values())
maxwidth = max(xcoords) + max_label_size + max_slabel_size
maxheight = max(ycoords) + .5 * yscale
# initialize canvas
if canvas is None:
canvas = svg.Svg(util.open_stream(filename, "w"))
width = int(rmargin + maxwidth + lmargin)
height = int(tmargin + maxheight + bmargin)
canvas.beginSvg(width, height)
canvas.beginStyle("font-family: \"Sans\";")
if autoclose == None:
autoclose = True
else:
if autoclose == None:
autoclose = False
canvas.beginTransform(("translate", lmargin, tmargin))
draw_stree(canvas,
stree,
slayout,
yscale=yscale,
stree_width=stree_width,
stree_color=stree_color,
snode_color=snode_color)
# draw stree leaves
for node in stree:
x, y = slayout[node]
if node.is_leaf():
canvas.text(snames[node.name],
x + leaf_padding + max_label_size,
y + stree_font_size / 2.,
stree_font_size,
fillColor=snode_color)
# draw tree
for node in tree:
containsL = containsLoss(node, brecon)
for n in range(len(brecon[node])):
# print brecon[node]
x, y = layout[node][n]
# print layout[node]
if containsL == False:
px, py = layout[node.parent][-1]
else:
if brecon[node][n][1] == "loss":
px, py = layout[node.parent][-1]
else:
px, py = layout[node][n - 1]
trans = False
if node.parent:
for ev in brecon[node]:
snode, event, frequency = ev
psnode = brecon[node.parent][-1][0]
while snode:
if psnode == snode:
break
snode = snode.parent
else:
trans = True
if not trans:
canvas.line(x, y, px, py, color=tree_color)
else:
arch = 20
x2 = (x * .5 + px * .5) - arch
y2 = (y * .5 + py * .5)
x3 = (x * .5 + px * .5) - arch
y3 = (y * .5 + py * .5)
canvas.write("<path d='M%f %f C%f %f %f %f %f %f' %s />\n " %
(x, y, x2, y2, x3, y3, px, py,
" style='stroke-dasharray: 4, 2' " +
svg.colorFields(tree_trans_color, (0, 0, 0, 0))))
# draw events
for node in tree:
for n in range(len(brecon[node])):
snode, event, frequency = brecon[node][n]
x, y = layout[node][n]
o = event_size / 2.0
if event == "loss":
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=loss_color,
strokeColor=loss_color_border)
canvas.text(frequency,
x - o,
y - o,
font_size,
fillColor=(1, 1, 1))
if event == "spec":
canvas.text(frequency,
slayout[snode][0] - leaf_padding / 2,
slayout[snode][1] - font_size,
font_size,
fillColor=(0, 0, 0))
if event == "dup":
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=dup_color,
strokeColor=dup_color_border)
canvas.text(frequency,
x - o,
y - o,
font_size,
fillColor=dup_color)
elif event == "trans":
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=trans_color,
strokeColor=trans_color_border)
canvas.text(frequency,
x - o,
y - o,
font_size,
fillColor=trans_color)
# draw tree leaves
for node in tree:
for n in range(len(brecon[node])):
x, y = layout[node][n]
if node.is_leaf() and containsLoss(node, brecon) == False:
canvas.text(node.name,
x + leaf_padding,
y + font_size / 2.,
font_size,
fillColor=(0, 0, 0))
canvas.endTransform()
if autoclose:
canvas.endStyle()
canvas.endSvg()
return canvas
def draw_tree(tree,
stree,
extra,
xscale=100,
yscale=100,
leaf_padding=10,
label_size=None,
label_offset=None,
font_size=12,
stree_font_size=20,
canvas=None,
autoclose=True,
rmargin=10,
lmargin=10,
tmargin=0,
bmargin=0,
stree_color=(.4, .4, 1),
snode_color=(.2, .2, .7),
event_size=10,
rootlen=None,
stree_width=.8,
filename=sys.stdout,
labels=None,
slabels=None):
recon = extra["species_map"]
loci = extra["locus_map"]
order = extra["order"]
# setup color map
all_loci = sorted(set(loci.values()))
num_loci = len(all_loci)
colormap = util.rainbow_color_map(low=0, high=num_loci - 1)
locus_color = {}
for ndx, locus in enumerate(all_loci):
locus_color[locus] = colormap.get(ndx)
# set defaults
font_ratio = 8. / 11.
if label_size is None:
label_size = .7 * font_size
#if label_offset is None:
# label_offset = -1
if sum(x.dist for x in tree.nodes.values()) == 0:
legend_scale = False
minlen = xscale
snames = dict((x, x) for x in stree.leaf_names())
if labels is None:
labels = {}
if slabels is None:
slabels = {}
# layout stree
slayout = treelib.layout_tree(stree, xscale, yscale)
if rootlen is None:
rootlen = .1 * max(l[0] for l in slayout.values())
# setup slayout
x, y = slayout[stree.root]
slayout[None] = (x - rootlen, y)
for node, (x, y) in slayout.items():
slayout[node] = (x + rootlen, y - .5 * yscale)
# layout tree
ylists = defaultdict(lambda: [])
yorders = {}
# layout speciations and genes (y)
events = phylo.label_events(tree, recon)
for node in tree.preorder():
snode = recon[node]
event = events[node]
if event == "spec" or event == "gene":
yorders[node] = len(ylists[snode])
ylists[snode].append(node)
# layout internal nodes (y)
for node in tree.postorder():
snode = recon[node]
event = events[node]
if event != "spec" and event != "gene":
v = [yorders[child] for child in node.children]
yorders[node] = stats.mean(v)
# layout node (x)
xorders = {}
xmax = defaultdict(lambda: 0)
for node in tree.postorder():
snode = recon[node]
event = events[node]
if event == "spec" or event == "gene":
xorders[node] = 0
else:
v = [xorders[child] for child in node.children]
xorders[node] = max(v) + 1
xmax[snode] = max(xmax[snode], xorders[node])
## # initial order
## xpreorders = {}
## for node in tree.postorder():
## snode = recon[node]
## event = events[node]
## if event == "spec" or event == "gene":
## xpreorders[node] = 0
## else:
## v = [xpreorders[child] for child in node.children]
## xpreorders[node] = max(v) + 1
#### print node.name, xpreorders[node]
## # hack-ish approach : shift x until order is satisfied
## def shift(node, x):
## xpreorders[node] += x
## for child in node.children:
## if events[child] != "spec":
## shift(child, x)
## satisfied = False
## while not satisfied:
## satisfied = True
## for snode, d in order.iteritems():
## for plocus, lst in d.iteritems():
## # test each pair
## for m, node1 in enumerate(lst):
## x1 = xpreorders[node1]
## for node2 in lst[m+1:]:
## x2 = xpreorders[node2]
#### print node1, node2, x1, x2
## if x2 < x1:
## # violation - shift all descendants in the sbranch
## satisfied = False
#### print 'violation', node1, node2, x1, x2, x1-x2+1
## shift(node2, x1-x2+1)
## break
## # finally, "normalize" xorders
## xorders = {}
## xmax = defaultdict(lambda: 0)
## for node in tree.postorder():
## snode = recon[node]
## xorders[node] = xpreorders[node]
## xmax[snode] = max(xmax[snode], xorders[node])
#### print node.name, xpreorders[node]
# setup layout
layout = {None: slayout[None]}
for node in tree:
snode = recon[node]
nx, ny = slayout[snode]
px, py = slayout[snode.parent]
# calc x
frac = (xorders[node]) / float(xmax[snode] + 1)
deltax = nx - px
x = nx - frac * deltax
# calc y
deltay = ny - py
slope = deltay / float(deltax)
deltax2 = x - px
deltay2 = slope * deltax2
offset = py + deltay2
frac = (yorders[node] + 1) / float(max(len(ylists[snode]), 1) + 1)
y = offset + (frac - .5) * stree_width * yscale
layout[node] = (x, y)
## if y > max(l[1] for l in slayout.values()) + 50:
## print nx, ny
## print px, py
## print offset, frac
## print ylists[snode], yorders[node]
## print node, snode, layout[node]
# layout label sizes
max_label_size = max(len(x.name)
for x in tree.leaves()) * font_ratio * font_size
max_slabel_size = max(
len(x.name) for x in stree.leaves()) * font_ratio * stree_font_size
xcoords, ycoords = zip(*slayout.values())
maxwidth = max(xcoords) + max_label_size + max_slabel_size
maxheight = max(ycoords) + .5 * yscale
# initialize canvas
if canvas is None:
canvas = svg.Svg(util.open_stream(filename, "w"))
width = int(rmargin + maxwidth + lmargin)
height = int(tmargin + maxheight + bmargin)
canvas.beginSvg(width, height)
canvas.beginStyle("font-family: \"Sans\";")
if autoclose == None:
autoclose = True
else:
if autoclose == None:
autoclose = False
canvas.beginTransform(("translate", lmargin, tmargin))
draw_stree(canvas,
stree,
slayout,
yscale=yscale,
stree_width=stree_width,
stree_color=stree_color,
snode_color=snode_color,
slabels=slabels)
# draw stree leaves
for node in stree:
x, y = slayout[node]
if node.is_leaf():
canvas.text(snames[node.name],
x + leaf_padding + max_label_size,
y + stree_font_size / 2.,
stree_font_size,
fillColor=snode_color)
# draw tree
for node in tree:
x, y = layout[node]
px, py = layout[node.parent]
if node.parent:
color = locus_color[loci[node.parent]]
else:
color = locus_color[loci[tree.root]]
canvas.line(x, y, px, py, color=color)
# draw tree names
for node in tree:
x, y = layout[node]
px, py = layout[node.parent]
if node.is_leaf():
canvas.text(node.name,
x + leaf_padding,
y + font_size / 2.,
font_size,
fillColor=(0, 0, 0))
if node.name in labels:
canvas.text(labels[node.name],
x,
y,
label_size,
fillColor=(0, 0, 0))
# draw events
for node in tree:
if node.parent:
locus = loci[node]
plocus = loci[node.parent]
if locus != plocus:
color = locus_color[locus]
x, y = layout[node]
o = event_size / 2.0
canvas.rect(x - o,
y - o,
event_size,
event_size,
fillColor=color,
strokeColor=color)
canvas.endTransform()
if autoclose:
canvas.endStyle()
canvas.endSvg()
return canvas