def epoch(args):
"""
%prog epoch
Illustrate the methods used in Maggie's epoch paper, in particular, how to
classifiy S/G/F/FB/FN for the genes.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (6, 4))
root = fig.add_axes([0, 0, 1, 1])
# Separators
linestyle = dict(lw=2, color="b", alpha=.2, zorder=2)
root.plot((0, 1), (.5, .5), "--", **linestyle)
for i in (1. / 3, 2. / 3):
root.plot((i, i), (.5, 1), "--", **linestyle)
for i in (1. / 6, 3. / 6, 5. / 6):
root.plot((i, i), (0, .5), "--", **linestyle)
# Diagrams
plot_diagram(root, 1. / 6, 3. / 4, "S", "syntenic")
plot_diagram(root, 3. / 6, 3. / 4, "F", "missing, with both flankers")
plot_diagram(root, 5. / 6, 3. / 4, "G", "missing, with one flanker")
plot_diagram(root, 2. / 6, 1. / 4, "FB", "has non-coding matches")
plot_diagram(root, 4. / 6, 1. / 4, "FN", "syntenic region has gap")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def scenario(args):
"""
%prog scenario
Illustration of the two-step genome merger process for B. rapa companion paper.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
# Layout format: (x, y, label, (chr lengths))
anc = (0.5, 0.9, "Ancestor", (1, ))
s1 = (0.2, 0.6, "Genome I", (1, ))
s2 = (0.5, 0.6, "Genome II", (1, ))
s3 = (0.8, 0.6, "Genome III", (1, ))
tetra = (0.35, 0.4, "Tetraploid I / II", (0.5, 0.9))
hexa = (0.5, 0.1, "Hexaploid I / II / III", (0.36, 0.46, 0.9))
labels = (anc, s1, s2, s3, tetra, hexa)
connections = (
(anc, s1),
(anc, s2),
(anc, s3),
(s1, tetra),
(s2, tetra),
(tetra, hexa),
(s3, hexa),
)
xinterval = 0.02
yratio = 0.05
for xx, yy, label, chrl in labels:
# RoundLabel(root, xx, yy, label)
root.text(xx, yy, label, ha="center", va="center")
offset = len(label) * 0.012
for i, c in enumerate(chrl):
ya = yy + yratio * c
yb = yy - yratio * c
Chromosome(root, xx - offset + i * xinterval, ya, yb, width=0.01)
# Comments
comments = ((0.15, 0.33, "II dominant"), (0.25, 0.03, "III dominant"))
for xx, yy, c in comments:
root.text(xx, yy, c, size=9, ha="center", va="center")
# Branches
tip = 0.04
for a, b in connections:
xa, ya, la, chra = a
xb, yb, lb, chrb = b
plt.plot((xa, xb), (ya - tip, yb + 2 * tip), "k-", lw=2, alpha=0.5)
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def epoch(args):
"""
%prog epoch
Illustrate the methods used in Maggie's epoch paper, in particular, how to
classifiy S/G/F/FB/FN for the genes.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (6, 4))
root = fig.add_axes([0, 0, 1, 1])
# Separators
linestyle = dict(lw=2, color="b", alpha=.2, zorder=2)
root.plot((0, 1), (.5, .5), "--", **linestyle)
for i in (1./3, 2./3):
root.plot((i, i), (.5, 1), "--", **linestyle)
for i in (1./6, 3./6, 5./6):
root.plot((i, i), (0, .5), "--", **linestyle)
# Diagrams
plot_diagram(root, 1./6, 3./4, "S", "syntenic")
plot_diagram(root, 3./6, 3./4, "F", "missing, with both flankers")
plot_diagram(root, 5./6, 3./4, "G", "missing, with one flanker")
plot_diagram(root, 2./6, 1./4, "FB", "has non-coding matches")
plot_diagram(root, 4./6, 1./4, "FN", "syntenic region has gap")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def scenario(args):
"""
%prog scenario
Illustration of the two-step genome merger process for B. rapa companion paper.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
# Layout format: (x, y, label, (chr lengths))
anc = (.5, .9, "Ancestor", (1,))
s1 = (.2, .6, "Genome I", (1,))
s2 = (.5, .6, "Genome II", (1,))
s3 = (.8, .6, "Genome III", (1,))
tetra = (.35, .4, "Tetraploid I / II", (.5, .9))
hexa = (.5, .1, "Hexaploid I / II / III", (.36, .46, .9))
labels = (anc, s1, s2, s3, tetra, hexa)
connections = ((anc, s1), (anc, s2), (anc, s3),\
(s1, tetra), (s2, tetra),
(tetra, hexa), (s3, hexa))
xinterval = .02
yratio = .05
for xx, yy, label, chrl in labels:
#RoundLabel(root, xx, yy, label)
root.text(xx, yy, label, ha="center", va="center")
offset = len(label) * .012
for i, c in enumerate(chrl):
ya = yy + yratio * c
yb = yy - yratio * c
Chromosome(root, xx - offset + i * xinterval, ya, yb, width=.01)
# Comments
comments = ((.15, .33, "II dominant"),
(.25, .03, "III dominant"))
for xx, yy, c in comments:
root.text(xx, yy, c, size=9, ha="center", va="center")
# Branches
tip = .04
for a, b in connections:
xa, ya, la, chra = a
xb, yb, lb, chrb = b
plt.plot((xa, xb), (ya - tip, yb + 2 * tip), 'k-', lw=2, alpha=.5)
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def excision(args):
"""
%prog excision
Illustrate the mechanism of illegitimate recombination.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args(args)
fig = plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
plt.plot((.2, .8), (.6, .6), 'r-', lw=3)
plt.plot((.4, .6), (.6, .6), 'b>-', mfc='g', mec='w', ms=12, lw=3)
plt.plot((.3, .7), (.5, .5), 'r-', lw=3)
plt.plot((.5, ), (.5, ), 'b>-', mfc='g', mec='w', ms=12, lw=3)
# Circle excision
plt.plot((.5, ), (.45, ), 'b>-', mfc='g', mec='w', ms=12, lw=3)
circle = CirclePolygon((.5, .4), .05, fill=False, lw=3, ec="b")
root.add_patch(circle)
arrow_dist = .07
ar_xpos, ar_ypos = .5, .52
root.annotate(" ", (ar_xpos, ar_ypos),
(ar_xpos, ar_ypos + arrow_dist),
arrowprops=arrowprops)
RoundLabel(root, .2, .64, "Gene")
RoundLabel(root, .3, .54, "Excision")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def excision(args):
"""
%prog excision
Illustrate the mechanism of illegitimate recombination.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args(args)
fig = plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
plt.plot((0.2, 0.8), (0.6, 0.6), "r-", lw=3)
plt.plot((0.4, 0.6), (0.6, 0.6), "b>-", mfc="g", mec="w", ms=12, lw=3)
plt.plot((0.3, 0.7), (0.5, 0.5), "r-", lw=3)
plt.plot((0.5, ), (0.5, ), "b>-", mfc="g", mec="w", ms=12, lw=3)
# Circle excision
plt.plot((0.5, ), (0.45, ), "b>-", mfc="g", mec="w", ms=12, lw=3)
circle = CirclePolygon((0.5, 0.4), 0.05, fill=False, lw=3, ec="b")
root.add_patch(circle)
arrow_dist = 0.07
ar_xpos, ar_ypos = 0.5, 0.52
root.annotate(" ", (ar_xpos, ar_ypos), (ar_xpos, ar_ypos + arrow_dist),
arrowprops=arrowprops)
RoundLabel(root, 0.2, 0.64, "Gene")
RoundLabel(root, 0.3, 0.54, "Excision")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def bites(args):
"""
%prog bites
Illustrate the pipeline for automated bite discovery.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (6, 6))
root = fig.add_axes([0, 0, 1, 1])
# HSP pairs
hsps = (((50, 150), (60, 180)),
((190, 250), (160, 235)),
((300, 360), (270, 330)),
((430, 470), (450, 490)),
((570, 620), (493, 543)),
((540, 555), (370, 385)), # non-collinear hsps
)
titlepos = (.9, .65, .4)
titles = ("Compare orthologous region",
"Find collinear HSPs",
"Scan paired gaps")
ytip = .01
mrange = 650.
m = lambda x: x / mrange * .7 + .1
for i, (ya, title) in enumerate(zip(titlepos, titles)):
yb = ya - .1
plt.plot((.1, .8), (ya, ya), "-", color="gray", lw=2, zorder=1)
plt.plot((.1, .8), (yb, yb), "-", color="gray", lw=2, zorder=1)
RoundLabel(root, .5, ya + 4 * ytip, title)
root.text(.9, ya, "A. thaliana", ha="center", va="center")
root.text(.9, yb, "B. rapa", ha="center", va="center")
myhsps = hsps
if i >= 1:
myhsps = hsps[:-1]
for (a, b), (c, d) in myhsps:
a, b, c, d = [m(x) for x in (a, b, c, d)]
r1 = Rectangle((a, ya - ytip), b - a, 2 * ytip, fc='r', lw=0, zorder=2)
r2 = Rectangle((c, yb - ytip), d - c, 2 * ytip, fc='r', lw=0, zorder=2)
r3 = Rectangle((a, ya - ytip), b - a, 2 * ytip, fill=False, zorder=3)
r4 = Rectangle((c, yb - ytip), d - c, 2 * ytip, fill=False, zorder=3)
r5 = Polygon(((a, ya - ytip), (c, yb + ytip),
(d, yb + ytip), (b, ya - ytip)),
fc='r', alpha=.2)
rr = (r1, r2, r3, r4, r5)
if i == 2:
rr = rr[:-1]
for r in rr:
root.add_patch(r)
# Gap pairs
hspa, hspb = zip(*myhsps)
gapa, gapb = [], []
for (a, b), (c, d) in pairwise(hspa):
gapa.append((b + 1, c - 1))
for (a, b), (c, d) in pairwise(hspb):
gapb.append((b + 1, c - 1))
gaps = zip(gapa, gapb)
tpos = titlepos[-1]
yy = tpos - .05
for i, ((a, b), (c, d)) in enumerate(gaps):
i += 1
a, b, c, d = [m(x) for x in (a, b, c, d)]
xx = (a + b + c + d) / 4
TextCircle(root, xx, yy, str(i))
# Bites
ystart = .24
ytip = .05
bites = (("Bite(40=>-15)", True),
("Bite(50=>35)", False),
("Bite(70=>120)", False),
("Bite(100=>3)", True))
for i, (bite, selected) in enumerate(bites):
xx = .15 if (i % 2 == 0) else .55
yy = ystart - i / 2 * ytip
i += 1
TextCircle(root, xx, yy, str(i))
color = "k" if selected else "gray"
root.text(xx + ytip, yy, bite, size=10, color=color, va="center")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def bites(args):
"""
%prog bites
Illustrate the pipeline for automated bite discovery.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args()
fig = plt.figure(1, (6, 6))
root = fig.add_axes([0, 0, 1, 1])
# HSP pairs
hsps = (
((50, 150), (60, 180)),
((190, 250), (160, 235)),
((300, 360), (270, 330)),
((430, 470), (450, 490)),
((570, 620), (493, 543)),
((540, 555), (370, 385)), # non-collinear hsps
)
titlepos = (0.9, 0.65, 0.4)
titles = ("Compare orthologous region", "Find collinear HSPs",
"Scan paired gaps")
ytip = 0.01
mrange = 650.0
m = lambda x: x / mrange * 0.7 + 0.1
for i, (ya, title) in enumerate(zip(titlepos, titles)):
yb = ya - 0.1
plt.plot((0.1, 0.8), (ya, ya), "-", color="gray", lw=2, zorder=1)
plt.plot((0.1, 0.8), (yb, yb), "-", color="gray", lw=2, zorder=1)
RoundLabel(root, 0.5, ya + 4 * ytip, title)
root.text(0.9, ya, "A. thaliana", ha="center", va="center")
root.text(0.9, yb, "B. rapa", ha="center", va="center")
myhsps = hsps
if i >= 1:
myhsps = hsps[:-1]
for (a, b), (c, d) in myhsps:
a, b, c, d = [m(x) for x in (a, b, c, d)]
r1 = Rectangle((a, ya - ytip),
b - a,
2 * ytip,
fc="r",
lw=0,
zorder=2)
r2 = Rectangle((c, yb - ytip),
d - c,
2 * ytip,
fc="r",
lw=0,
zorder=2)
r3 = Rectangle((a, ya - ytip),
b - a,
2 * ytip,
fill=False,
zorder=3)
r4 = Rectangle((c, yb - ytip),
d - c,
2 * ytip,
fill=False,
zorder=3)
r5 = Polygon(
((a, ya - ytip), (c, yb + ytip), (d, yb + ytip),
(b, ya - ytip)),
fc="r",
alpha=0.2,
)
rr = (r1, r2, r3, r4, r5)
if i == 2:
rr = rr[:-1]
for r in rr:
root.add_patch(r)
# Gap pairs
hspa, hspb = zip(*myhsps)
gapa, gapb = [], []
for (a, b), (c, d) in pairwise(hspa):
gapa.append((b + 1, c - 1))
for (a, b), (c, d) in pairwise(hspb):
gapb.append((b + 1, c - 1))
gaps = zip(gapa, gapb)
tpos = titlepos[-1]
yy = tpos - 0.05
for i, ((a, b), (c, d)) in enumerate(gaps):
i += 1
a, b, c, d = [m(x) for x in (a, b, c, d)]
xx = (a + b + c + d) / 4
TextCircle(root, xx, yy, str(i))
# Bites
ystart = 0.24
ytip = 0.05
bites = (
("Bite(40=>-15)", True),
("Bite(50=>35)", False),
("Bite(70=>120)", False),
("Bite(100=>3)", True),
)
for i, (bite, selected) in enumerate(bites):
xx = 0.15 if (i % 2 == 0) else 0.55
yy = ystart - i / 2 * ytip
i += 1
TextCircle(root, xx, yy, str(i))
color = "k" if selected else "gray"
root.text(xx + ytip, yy, bite, size=10, color=color, va="center")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
