def getBranchNames(self, lines=None):
"""Get numbering of ancestral nodes"""
lines = self.setupLines(lines)
for line in lines:
if line.startswith("(1) Branch lengths and substitution pattern"):
break
else:
raise Exception("no branch names found")
branches = lines.next().strip().split()
names = [branch.split("..") for branch in branches]
dists = map(float, lines.next().strip().split())
# add nodes to tree
tree = treelib.Tree()
for name in set(util.flatten(names)):
tree.add(treelib.TreeNode(name))
# link up nodes
for (top, bot), dist in zip(names, dists):
tree.add_child(tree.nodes[top], tree.nodes[bot])
tree.nodes[bot].dist = dist
# find root
for node in tree:
if node.parent is None:
tree.root = node
break
return tree
def getBranchNames(self, lines=None):
"""Get numbering of ancestral nodes"""
lines = self.setupLines(lines)
for line in lines:
if line.startswith("(1) Branch lengths and substitution pattern"):
break
else:
raise Exception("no branch names found")
branches = lines.next().strip().split()
names = [branch.split("..") for branch in branches]
dists = map(float, lines.next().strip().split())
# add nodes to tree
tree = treelib.Tree()
for name in set(util.flatten(names)):
tree.add(treelib.TreeNode(name))
# link up nodes
for (top, bot), dist in zip(names, dists):
tree.add_child(tree.nodes[top], tree.nodes[bot])
tree.nodes[bot].dist = dist
# find root
for node in tree:
if node.parent is None:
tree.root = node
break
return tree
def confusionMatrix(parts1, parts2):
"""
Returns a confusion matrix of two different partitions of the same items.
"""
confuse = util.Dict(dim=2, default=0)
lookup1 = item2part(parts1)
lookup2 = item2part(parts2)
items1 = set(util.flatten(parts1, 1))
items2 = set(util.flatten(parts2, 1))
sameset = items1 & items2
diffset = items1.symmetric_difference(items2)
for item in sameset:
confuse[lookup1[item]][lookup2[item]] += 1
return confuse, list(diffset)
def confusionMatrix(parts1, parts2):
"""Returns a confusion matrix of two different partitions of the same
items"""
confuse = util.Dict(dim=2, default=0)
lookup1 = item2part(parts1)
lookup2 = item2part(parts2)
items1 = set(util.flatten(parts1, 1))
items2 = set(util.flatten(parts2, 1))
sameset = items1 & items2
diffset = items1.symmetric_difference(items2)
for item in sameset:
confuse[lookup1[item]][lookup2[item]] += 1
return confuse, list(diffset)
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 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):
from rasmus import util
# determine filename
if filename == None:
filename = util.tempfile(".", "heatmap", ".svg")
temp = True
else:
temp = False
# determine colormap
if colormap == 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
color = colormap.get(matrix[i][j])
s.rect(xstart + xdir*j*width,
ystart + ydir*i*height,
xdir*width, ydir*height, color, 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)
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*width,
ystart + ydir*(i+yoffset)*height +
height/2.0 + textsize/2.0,
textsize,
fillColor=valColor)
# draw labels
if rlabels != 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 != 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
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)
