def estimategaps(args):
"""
%prog estimategaps JM-4 chr1 JMMale-1
Illustrate ALLMAPS gap estimation algorithm.
"""
p = OptionParser(estimategaps.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="6x6", dpi=300)
if len(args) != 3:
sys.exit(not p.print_help())
pf, seqid, mlg = args
bedfile = pf + ".lifted.bed"
agpfile = pf + ".agp"
function = lambda x: x.cm
cc = Map(bedfile, scaffold_info=True, function=function)
agp = AGP(agpfile)
g = GapEstimator(cc, agp, seqid, mlg, function=function)
pp, chrsize, mlgsize = g.pp, g.chrsize, g.mlgsize
spl, spld = g.spl, g.spld
g.compute_all_gaps(verbose=False)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Panel A
xstart, ystart = 0.15, 0.65
w, h = 0.7, 0.3
t = np.linspace(0, chrsize, 1000)
ax = fig.add_axes([xstart, ystart, w, h])
mx, my = zip(*g.scatter_data)
rho = spearmanr(mx, my)
dsg = "g"
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(mx, my, ".", color=set2[3])
ax.plot(t, spl(t), "-", color=dsg)
ax.text(0.05, 0.95, mlg, va="top", transform=ax.transAxes)
normalize_lms_axis(ax, xlim=chrsize, ylim=mlgsize, ylabel="Genetic distance (cM)")
if rho < 0:
ax.invert_yaxis()
# Panel B
ystart -= 0.28
h = 0.25
ax = fig.add_axes([xstart, ystart, w, h])
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(t, spld(t), "-", lw=2, color=dsg)
ax.plot(pp, spld(pp), "o", mfc="w", mec=dsg, ms=5)
normalize_lms_axis(
ax,
xlim=chrsize,
ylim=25 * 1e-6,
xfactor=1e-6,
xlabel="Physical position (Mb)",
yfactor=1000000,
ylabel="Recomb. rate\n(cM / Mb)",
)
ax.xaxis.grid(False)
# Panel C (specific to JMMale-1)
a, b = "scaffold_1076", "scaffold_861"
sizes = dict(
(x.component_id, (x.object_beg, x.object_end, x.component_span, x.orientation))
for x in g.agp
if not x.is_gap
)
a_beg, a_end, asize, ao = sizes[a]
b_beg, b_end, bsize, bo = sizes[b]
gapsize = g.get_gapsize(a)
total_size = asize + gapsize + bsize
ratio = 0.6 / total_size
y = 0.16
pad = 0.03
pb_ratio = w / chrsize
# Zoom
lsg = "lightslategray"
root.plot((0.15 + pb_ratio * a_beg, 0.2), (ystart, ystart - 0.14), ":", color=lsg)
root.plot((0.15 + pb_ratio * b_end, 0.3), (ystart, ystart - 0.08), ":", color=lsg)
ends = []
for tag, size, marker, beg in zip(
(a, b), (asize, bsize), (49213, 81277), (0.2, 0.2 + (asize + gapsize) * ratio)
):
end = beg + size * ratio
marker = beg + marker * ratio
ends.append((beg, end, marker))
root.plot((marker,), (y,), "o", color=lsg)
root.text((beg + end) / 2, y + pad, latex(tag), ha="center", va="center")
HorizontalChromosome(root, beg, end, y, height=0.025, fc="gainsboro")
begs, ends, markers = zip(*ends)
fontprop = dict(color=lsg, ha="center", va="center")
ypos = y + pad * 2
root.plot(markers, (ypos, ypos), "-", lw=2, color=lsg)
root.text(
sum(markers) / 2,
ypos + pad,
"Distance: 1.29cM $\Leftrightarrow$ 211,824bp (6.1 cM/Mb)",
**fontprop
)
ypos = y - pad
xx = markers[0], ends[0]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "34,115bp", **fontprop)
xx = markers[1], begs[1]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "81,276bp", **fontprop)
root.plot((ends[0], begs[1]), (y, y), ":", lw=2, color=lsg)
root.text(
sum(markers) / 2,
ypos - 3 * pad,
r"$\textit{Estimated gap size: 96,433bp}$",
color="r",
ha="center",
va="center",
)
labels = ((0.05, 0.95, "A"), (0.05, 0.6, "B"), (0.05, 0.27, "C"))
panel_labels(root, labels)
normalize_axes(root)
pf = "estimategaps"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def estimategaps(args):
"""
%prog estimategaps JM-4 chr1 JMMale-1
Illustrate ALLMAPS gap estimation algorithm.
"""
p = OptionParser(estimategaps.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="6x6", dpi=300)
if len(args) != 3:
sys.exit(not p.print_help())
pf, seqid, mlg = args
bedfile = pf + ".lifted.bed"
agpfile = pf + ".agp"
function = lambda x: x.cm
cc = Map(bedfile, scaffold_info=True, function=function)
agp = AGP(agpfile)
g = GapEstimator(cc, agp, seqid, mlg, function=function)
pp, chrsize, mlgsize = g.pp, g.chrsize, g.mlgsize
spl, spld = g.spl, g.spld
g.compute_all_gaps(verbose=False)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Panel A
xstart, ystart = .15, .65
w, h = .7, .3
t = np.linspace(0, chrsize, 1000)
ax = fig.add_axes([xstart, ystart, w, h])
mx, my = zip(*g.scatter_data)
rho = spearmanr(mx, my)
dsg = "g"
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(mx, my, ".", color=set2[3])
ax.plot(t, spl(t), "-", color=dsg)
ax.text(.05, .95, mlg, va="top", transform=ax.transAxes)
normalize_lms_axis(ax, xlim=chrsize, ylim=mlgsize,
ylabel="Genetic distance (cM)")
if rho < 0:
ax.invert_yaxis()
# Panel B
ystart -= .28
h = .25
ax = fig.add_axes([xstart, ystart, w, h])
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(t, spld(t), "-", lw=2, color=dsg)
ax.plot(pp, spld(pp), "o", mfc="w", mec=dsg, ms=5)
normalize_lms_axis(ax, xlim=chrsize, ylim=25 * 1e-6,
xfactor=1e-6, xlabel="Physical position (Mb)",
yfactor=1000000, ylabel="Recomb. rate\n(cM / Mb)")
# Panel C (specific to JMMale-1)
a, b = "scaffold_1076", "scaffold_861"
sizes = dict((x.component_id, (x.object_beg, x.object_end,
x.component_span, x.orientation)) \
for x in g.agp if not x.is_gap)
a_beg, a_end, asize, ao = sizes[a]
b_beg, b_end, bsize, bo = sizes[b]
gapsize = g.get_gapsize(a)
total_size = asize + gapsize + bsize
ratio = .6 / total_size
y = .16
pad = .03
pb_ratio = w / chrsize
# Zoom
lsg = "lightslategray"
root.plot((.15 + pb_ratio * a_beg, .2),
(ystart, ystart - .14), ":", color=lsg)
root.plot((.15 + pb_ratio * b_end, .3),
(ystart, ystart - .08), ":", color=lsg)
ends = []
for tag, size, marker, beg in zip((a, b), (asize, bsize), (49213, 81277),
(.2, .2 + (asize + gapsize) * ratio)):
end = beg + size * ratio
marker = beg + marker * ratio
ends.append((beg, end, marker))
root.plot((marker,), (y,), "o", color=lsg)
root.text((beg + end) / 2, y + pad, latex(tag),
ha="center", va="center")
HorizontalChromosome(root, beg, end, y, height=.025, fc='gainsboro')
begs, ends, markers = zip(*ends)
fontprop = dict(color=lsg, ha="center", va="center")
ypos = y + pad * 2
root.plot(markers, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(markers) / 2, ypos + pad,
"Distance: 1.29cM $\Leftrightarrow$ 211,824bp (6.1 cM/Mb)", **fontprop)
ypos = y - pad
xx = markers[0], ends[0]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "34,115bp", **fontprop)
xx = markers[1], begs[1]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "81,276bp", **fontprop)
root.plot((ends[0], begs[1]), (y, y), ":", lw=2, color=lsg)
root.text(sum(markers) / 2, ypos - 3 * pad, r"$\textit{Estimated gap size: 96,433bp}$",
color="r", ha="center", va="center")
labels = ((.05, .95, 'A'), (.05, .6, 'B'), (.05, .27, 'C'))
panel_labels(root, labels)
normalize_axes(root)
pf = "estimategaps"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)