def draw_sector(self, end):
"""draw the sector"""
segment = path.path(
path.arc(self.xo, self.yo, self.inner_r, self.start_angle,
self.end_angle),
path.arcn(self.xo, self.yo, self.sector_width + self.inner_r,
self.end_angle, self.start_angle), path.closepath())
self.shape_canvas.fill(segment, [self.sector_color])
# draw a delimiting line between sectors
line_color = color.gray(0.15)
if end and (self.end_angle - self.start_angle) < 0.25:
line_color = color.rgb.red
r = self.inner_r + self.sector_width
start_radians = self.start_angle * pi / 180.0
end_radians = self.end_angle * pi / 180.0
x0 = self.inner_r * cos(start_radians) + self.xo
y0 = self.inner_r * sin(start_radians) + self.yo
x1 = r * cos(start_radians) + self.xo
y1 = r * sin(start_radians) + self.yo
self.shape_canvas.stroke(path.line(x0, y0, x1, y1),
[style.linewidth(0.01), line_color])
x0 = self.inner_r * cos(end_radians) + self.xo
y0 = self.inner_r * sin(end_radians) + self.yo
x1 = r * cos(end_radians) + self.xo
y1 = r * sin(end_radians) + self.yo
self.shape_canvas.stroke(path.line(x0, y0, x1, y1),
[style.linewidth(0.01), line_color])
def draw_page(c, file, sensori, sensorj, nci, ncj, matrix):
"""
Generates the contingency table for the peaks
:param c:
:param file:
:param sensori:
:param sensorj:
:param nci:
:param ncj:
:return:
"""
for i in range(nci):
im = Image.open(resultpath+'/icons/'+"%s%s.cl%d.png"%(file, sensori, i+1))
image_bw = bitmap.image(im.size[0], im.size[1], im.mode, im.tostring())
bitmap_bw = bitmap.bitmap(0, i+1, image_bw, height=0.8)
c.insert(bitmap_bw)
for i in range(ncj):
im = Image.open(resultpath+'/icons/'+"%s%s.cl%d.png"%(file, sensorj, i+1))
image_bw = bitmap.image(im.size[0], im.size[1], im.mode, im.tostring())
bitmap_bw = bitmap.bitmap(i+1, 0, image_bw, height=0.8)
c.insert(bitmap_bw)
grad = np.zeros(matrix.shape)
for i in range(matrix.shape[0]):
grad[i] = matrix[i]/np.sum(matrix[i])
for i in range(nci):
for j in range(ncj):
p = path.rect(i+1, j+1, 1, 1)
c.stroke(p, [deco.filled([gray(1-grad[i, j])])])
c.text(i+1, j+1, str(int(matrix[i,j])), [text.size(-1), rgb.blue])
c.text(-1, (nci/2)+1, sensori, [text.size(-1)])
c.text((ncj/2)+1, -1, sensorj, [text.size(-1)])
# Margings for better printing
c.text(-1.5, (nci/2)+1, " ", [text.size(-1)])
c.text(nci+2, (nci/2)+1, " ", [text.size(-1)])
c.text((ncj/2)+1, -1.5, " ", [text.size(-1)])
c.text((ncj/2)+1, ncj+2, " ", [text.size(-1)])
def draw_page(c, file, sensori, sensorj, nci, ncj, matrix):
"""
Generates the contingency table for the peaks
:param c:
:param file:
:param sensori:
:param sensorj:
:param nci:
:param ncj:
:return:
"""
for i in range(nci):
im = Image.open(datainfo.dpath + '/' + datainfo.name +'/Results/icons/' + "%s%s.cl%d.png"%(file, sensori, i+1))
image_bw = bitmap.image(im.size[0], im.size[1], im.mode, im.tostring())
bitmap_bw = bitmap.bitmap(0, i+1, image_bw, height=0.8)
c.insert(bitmap_bw)
for i in range(ncj):
im = Image.open(datainfo.dpath + '/' + datainfo.name +'/Results/icons/' + "%s%s.cl%d.png"%(file, sensorj, i+1))
image_bw = bitmap.image(im.size[0], im.size[1], im.mode, im.tostring())
bitmap_bw = bitmap.bitmap(i+1, 0, image_bw, height=0.8)
c.insert(bitmap_bw)
grad = np.zeros(matrix.shape)
for i in range(matrix.shape[0]):
grad[i] = matrix[i]/np.sum(matrix[i])
for i in range(nci):
for j in range(ncj):
p = path.rect(i+1, j+1, 1, 1)
c.stroke(p, [deco.filled([gray(1-grad[i, j])])])
c.text(i+1, j+1, str(int(matrix[i,j])), [text.size(-1), rgb.blue])
c.text(-1, (nci/2)+1, sensori, [text.size(-1)])
c.text((ncj/2)+1, -1, sensorj, [text.size(-1)])
# Margings for better printing
c.text(-1.5, (nci/2)+1, " ", [text.size(-1)])
c.text(nci+2, (nci/2)+1, " ", [text.size(-1)])
c.text((ncj/2)+1, -1.5, " ", [text.size(-1)])
c.text((ncj/2)+1, ncj+2, " ", [text.size(-1)])
pyplot.show()
quit()
from pyx import canvas, graph, text, color, style, trafo, unit
from pyx.graph import axis, key
text.set(mode="latex")
text.preamble(r"\usepackage{txfonts}")
figwidth = 12
gkey = key.key(pos=None, hpos=0.05, vpos=0.8)
xaxis = axis.linear(title=r"Time, \(t\)")
yaxis = axis.linear(title="Signal", min=-5, max=17)
g = graph.graphxy(width=figwidth, x=xaxis, y=yaxis, key=gkey)
plotdata = [graph.data.values(x=t, y=signal+offset, title=label) for label, signal, offset in (r"\(A(t) = \mathrm{square}(2\pi t/T)\)", A, 2.5), (r"\(B(t) = \mathrm{sawtooth}(\phi + 2 \pi t/T)\)", B, -2.5)]
linestyles = [style.linestyle.solid, style.linejoin.round, style.linewidth.Thick, color.gradient.Rainbow, color.transparency(0.5)]
plotstyles = [graph.style.line(linestyles)]
g.plot(plotdata, plotstyles)
g.plot(graph.data.values(x=t, y=listX, title="Blah"), plotstyles)
g.text(10*unit.x_pt, 0.56*figwidth, r"\textbf{Cross correlation of noisy anharmonic signals}")
g.text(10*unit.x_pt, 0.33*figwidth, "Phase shift: input \(\phi = %.2f \,\pi\), recovered \(\phi = %.2f \,\pi\)" % (phase_shift/pi, recovered_phase_shift/pi))
xxaxis = axis.linear(title=r"Time Lag, \(\Delta t\)", min=-1.5, max=1.5)
yyaxis = axis.linear(title=r"\(A(t) \star B(t)\)")
gg = graph.graphxy(width=0.2*figwidth, x=xxaxis, y=yyaxis)
plotstyles = [graph.style.line(linestyles + [color.rgb(0.2,0.5,0.2)])]
#gg.plot(graph.data.values(x=dt, y=xcorr), plotstyles)
gg.plot(graph.data.values(x=dt, y=xcorr, title="Blah"), plotstyles)
gg.stroke(gg.xgridpath(recovered_time_shift), [style.linewidth.THIck, color.gray(0.5), color.transparency(0.7)])
ggtrafos = [trafo.translate(0.75*figwidth, 0.45*figwidth)]
g.insert(gg, ggtrafos)
g.writePDFfile("so-xcorr-pyx")
def special(self, s, fontmap):
x = self.pos[_POS_H] * self.pyxconv
y = -self.pos[_POS_V] * self.pyxconv
if self.debug:
self.debugfile.write("%d: xxx '%s'\n" % (self.filepos, s))
if not s.startswith("PyX:"):
logger.warning("ignoring special '%s'" % s)
return
# it is in general not safe to continue using the currently active font because
# the specials may involve some gsave/grestore operations
self.flushtext(fontmap)
command, args = s[4:].split()[0], s[4:].split()[1:]
if command == "color_begin":
if args[0] == "cmyk":
c = color.cmyk(float(args[1]), float(args[2]), float(args[3]), float(args[4]))
elif args[0] == "gray":
c = color.gray(float(args[1]))
elif args[0] == "hsb":
c = color.hsb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "rgb":
c = color.rgb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "RGB":
c = color.rgb(int(args[1])/255.0, int(args[2])/255.0, int(args[3])/255.0)
elif args[0] == "texnamed":
try:
c = getattr(color.cmyk, args[1])
except AttributeError:
raise RuntimeError("unknown TeX color '%s', aborting" % args[1])
elif args[0] == "pyxcolor":
# pyx.color.cmyk.PineGreen or
# pyx.color.cmyk(0,0,0,0.0)
pat = re.compile(r"(pyx\.)?(color\.)?(?P<model>(cmyk)|(rgb)|(grey)|(gray)|(hsb))[\.]?(?P<arg>.*)")
sd = pat.match(" ".join(args[1:]))
if sd:
sd = sd.groupdict()
if sd["arg"][0] == "(":
numpat = re.compile(r"[+-]?((\d+\.\d*)|(\d*\.\d+)|(\d+))([eE][+-]\d+)?")
arg = tuple([float(x[0]) for x in numpat.findall(sd["arg"])])
try:
c = getattr(color, sd["model"])(*arg)
except TypeError or AttributeError:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
try:
c = getattr(getattr(color, sd["model"]), sd["arg"])
except AttributeError:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
raise RuntimeError("cannot access PyX color '%s' in TeX, aborting" % " ".join(args[1:]))
else:
raise RuntimeError("color model '%s' cannot be handled by PyX, aborting" % args[0])
self.beginsubpage([c])
elif command == "color_end":
self.endsubpage()
elif command == "rotate_begin":
self.beginsubpage([trafo.rotate_pt(float(args[0]), x, y)])
elif command == "rotate_end":
self.endsubpage()
elif command == "scale_begin":
self.beginsubpage([trafo.scale_pt(float(args[0]), float(args[1]), x, y)])
elif command == "scale_end":
self.endsubpage()
elif command == "epsinclude":
# parse arguments
argdict = {}
for arg in args:
name, value = arg.split("=")
argdict[name] = value
# construct kwargs for epsfile constructor
epskwargs = {}
epskwargs["filename"] = argdict["file"]
epskwargs["bbox"] = bbox.bbox_pt(float(argdict["llx"]), float(argdict["lly"]),
float(argdict["urx"]), float(argdict["ury"]))
if "width" in argdict:
epskwargs["width"] = float(argdict["width"]) * unit.t_pt
if "height" in argdict:
epskwargs["height"] = float(argdict["height"]) * unit.t_pt
if "clip" in argdict:
epskwargs["clip"] = int(argdict["clip"])
self.actpage.insert(epsfile.epsfile(x * unit.t_pt, y * unit.t_pt, **epskwargs))
elif command == "marker":
if len(args) != 1:
raise RuntimeError("marker contains spaces")
for c in args[0]:
if c not in string.ascii_letters + string.digits + "@":
raise RuntimeError("marker contains invalid characters")
if args[0] in self.actpage.markers:
raise RuntimeError("marker name occurred several times")
self.actpage.markers[args[0]] = x * unit.t_pt, y * unit.t_pt
else:
raise RuntimeError("unknown PyX special '%s', aborting" % command)
def special(self, s, fontmap):
x = self.pos[_POS_H] * self.pyxconv
y = -self.pos[_POS_V] * self.pyxconv
if self.debug:
self.debugfile.write("%d: xxx '%s'\n" % (self.filepos, s))
if not s.startswith("PyX:"):
logger.warning("ignoring special '%s'" % s)
return
# it is in general not safe to continue using the currently active font because
# the specials may involve some gsave/grestore operations
self.flushtext(fontmap)
command, args = s[4:].split()[0], s[4:].split()[1:]
if command == "color_begin":
if args[0] == "cmyk":
c = color.cmyk(float(args[1]), float(args[2]), float(args[3]),
float(args[4]))
elif args[0] == "gray":
c = color.gray(float(args[1]))
elif args[0] == "hsb":
c = color.hsb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "rgb":
c = color.rgb(float(args[1]), float(args[2]), float(args[3]))
elif args[0] == "RGB":
c = color.rgb(
int(args[1]) / 255.0,
int(args[2]) / 255.0,
int(args[3]) / 255.0)
elif args[0] == "texnamed":
try:
c = getattr(color.cmyk, args[1])
except AttributeError:
raise RuntimeError("unknown TeX color '%s', aborting" %
args[1])
elif args[0] == "pyxcolor":
# pyx.color.cmyk.PineGreen or
# pyx.color.cmyk(0,0,0,0.0)
pat = re.compile(
r"(pyx\.)?(color\.)?(?P<model>(cmyk)|(rgb)|(grey)|(gray)|(hsb))[\.]?(?P<arg>.*)"
)
sd = pat.match(" ".join(args[1:]))
if sd:
sd = sd.groupdict()
if sd["arg"][0] == "(":
numpat = re.compile(
r"[+-]?((\d+\.\d*)|(\d*\.\d+)|(\d+))([eE][+-]\d+)?"
)
arg = tuple(
[float(x[0]) for x in numpat.findall(sd["arg"])])
try:
c = getattr(color, sd["model"])(*arg)
except TypeError or AttributeError:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting"
% " ".join(args[1:]))
else:
try:
c = getattr(getattr(color, sd["model"]), sd["arg"])
except AttributeError:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting"
% " ".join(args[1:]))
else:
raise RuntimeError(
"cannot access PyX color '%s' in TeX, aborting" %
" ".join(args[1:]))
else:
raise RuntimeError(
"color model '%s' cannot be handled by PyX, aborting" %
args[0])
self.beginsubpage([c])
elif command == "color_end":
self.endsubpage()
elif command == "rotate_begin":
self.beginsubpage([trafo.rotate_pt(float(args[0]), x, y)])
elif command == "rotate_end":
self.endsubpage()
elif command == "scale_begin":
self.beginsubpage(
[trafo.scale_pt(float(args[0]), float(args[1]), x, y)])
elif command == "scale_end":
self.endsubpage()
elif command == "epsinclude":
# parse arguments
argdict = {}
for arg in args:
name, value = arg.split("=")
argdict[name] = value
# construct kwargs for epsfile constructor
epskwargs = {}
epskwargs["filename"] = argdict["file"]
epskwargs["bbox"] = bbox.bbox_pt(float(argdict["llx"]),
float(argdict["lly"]),
float(argdict["urx"]),
float(argdict["ury"]))
if "width" in argdict:
epskwargs["width"] = float(argdict["width"]) * unit.t_pt
if "height" in argdict:
epskwargs["height"] = float(argdict["height"]) * unit.t_pt
if "clip" in argdict:
epskwargs["clip"] = int(argdict["clip"])
self.actpage.insert(
epsfile.epsfile(x * unit.t_pt, y * unit.t_pt, **epskwargs))
elif command == "marker":
if len(args) != 1:
raise RuntimeError("marker contains spaces")
for c in args[0]:
if c not in string.ascii_letters + string.digits + "@":
raise RuntimeError("marker contains invalid characters")
if args[0] in self.actpage.markers:
raise RuntimeError("marker name occurred several times")
self.actpage.markers[args[0]] = x * unit.t_pt, y * unit.t_pt
else:
raise RuntimeError("unknown PyX special '%s', aborting" % command)
def plot_scores(self,
fname,
binsize=10000,
show_lads=False,
show_dips=False,
show_means=False,
show_partitions=False):
"""Plot a PDF of score data with optional indicators of partitions, "
partition means, LADs, and DIPs."""
# Make sure that the PYX module is available
try:
from pyx import canvas, path, document, color, text, style
except ImportError:
self.logger.warn("The package pyx must be installed to plot data")
return None
# Make sure desired data is present
if self.focus != 'binned':
if (self.data is None or numpy.nanmin(self.data['score']) == 0):
self.logger.warn("Requested data is not available for "
"plotting")
return None
elif (self.binned is None or numpy.nanmin(self.binned['score']) == 0):
self.logger.warn("Requested binned data is not available for "
"plotting")
return None
self.logger.info("Plotting data")
# Determine which data to use
if self.focus == 'binned':
data = self.binned
chr_indices = self.bin_indices
else:
data = self.data
chr_indices = self.chr_indices
# Plot each chromosome on its own page
pages = []
for i in range(self.chroms.shape[0]):
valid = numpy.where(
numpy.logical_not(
numpy.isnan(
data['score'][chr_indices[i]:chr_indices[i + 1]])))[0]
valid += chr_indices[i]
# Skip chromosomes without valid data
if valid.shape[0] == 0:
continue
mids = (data['coords'][valid, 0] + data['coords'][valid, 1]) // 2
if binsize > 0:
# Bin data to the resolution requested
start = (mids[0] // binsize) * binsize
stop = (mids[-1] // binsize + 1) * binsize
indices = (mids - start) // binsize
counts = numpy.bincount(indices)
Ys = numpy.bincount(
indices, weights=data['score'][valid]) / numpy.maximum(
1, counts)
mids = (start + numpy.arange(
(stop - start) // binsize) * binsize + binsize / 2)
valid = numpy.where(counts > 0)[0]
Ys = Ys[valid]
mids = mids[valid]
coords = numpy.zeros((Ys.shape[0], 2), dtype=numpy.float64)
coords[:, 0] = start + valid * binsize
coords[:, 1] = start + valid * binsize + binsize
else:
Ys = data['score'][valid]
start = data['coords'][valid, 0]
stop = data['coords'][valid[-1], 1]
coords = data['coords'][valid, :].astype(numpy.float64)
c = canvas.canvas()
width = (stop - start) / 5000000.
height = 5.
maxscore = numpy.amax(numpy.abs(Ys))
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
maxscore = max(
maxscore,
numpy.amax(numpy.abs(self.partitions['score'][where])))
Ys /= maxscore
Ys *= height * 0.5
Xs = (mids - start) / float(stop - start) * width
coords -= start
coords /= (stop - start)
coords *= width
lpath = path.path(path.moveto(0, 0))
for j in range(valid.shape[0]):
if j == 0 or valid[j] - valid[j - 1] > 1:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(Xs[j], Ys[j]))
if j == Xs.shape[0] - 1 or valid[j + 1] - valid[j] > 1:
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
lpath.append(path.closepath())
# add lads if requests and already determined
if show_lads and self.LADs is not None:
where = numpy.where(self.LADs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.LADs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.LADs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.gray(0.85)])
# add dips if requests and already determined
if show_dips and self.DIPs is not None:
print(self.DIPs.shape)
where = numpy.where(self.DIPs['chr'] == i)[0]
if where.shape[0] == 0:
continue
for j in where:
X0 = ((self.DIPs['coords'][j, 0] - start) /
float(stop - start) * width)
X1 = ((self.DIPs['coords'][j, 1] - start) /
float(stop - start) * width)
c.fill(path.rect(X0, -height / 2, X1 - X0, height),
[color.rgb.red])
# add signal track
c.fill(lpath)
c.stroke(path.line(0, -height / 2, width, -height / 2))
# add partition mean line if requested and already determined
if show_means and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
Ys = ((self.partitions['score'][where] / maxscore) * height *
0.5)
lpath = path.path(path.moveto(0, 0))
for j in range(Ys.shape[0]):
if j == 0 or coords[j, 0] != coords[j - 1, 1]:
lpath.append(path.lineto(coords[j, 0], 0))
lpath.append(path.lineto(coords[j, 0], Ys[j]))
lpath.append(path.lineto(coords[j, 1], Ys[j]))
if (j == Ys.shape[0] - 1
or coords[j, 1] != coords[j + 1, 0]):
lpath.append(path.lineto(coords[j, 1], 0))
lpath.append(path.lineto(width, 0))
c.stroke(lpath, [
color.rgb.blue, style.linewidth.THIN,
color.transparency(0.5)
])
# add partition lines if requested and already determined
if show_partitions and self.partitions is not None:
where = numpy.where(self.partitions['chr'] == i)[0]
coords = ((self.partitions['coords'][where, :] - start) /
float(stop - start) * width)
for j in range(coords.shape[0] - 1):
c.stroke(
path.line(coords[j, 1], -height * 0.5, coords[j, 1],
height * 0.5), [style.linewidth.THin])
if coords[j, 1] != coords[j + 1, 0]:
c.stroke(
path.line(coords[j + 1, 0], -height * 0.5,
coords[j + 1, 0], height * 0.5),
[style.linewidth.THin])
# add coordinates
for j in range(int(numpy.ceil(start / 10000000.)),
int(numpy.floor(stop / 10000000.) + 1)):
X = (j * 10000000. - start) / (stop - start) * width
c.stroke(path.line(X, -height / 2, X, -height / 2 - 0.2))
c.text(X, -height / 2 - 0.25, "%i Mb" % (j * 10),
[text.halign.center, text.valign.top])
c.text(width * 0.5, -height / 2 - 0.6,
"%s" % self.chroms[i].replace('_', ' '),
[text.halign.center, text.valign.top])
pages.append(document.page(c))
doc = document.document(pages)
doc.writePDFfile(fname)
