def f3a(args):
"""
%prog f3a chrA02,A02,C2,chrC02 chr.sizes all.bed data
Napus Figure 3A displays alignments between quartet chromosomes, inset
with read histograms.
"""
from jcvi.formats.bed import Bed
p = OptionParser(f3a.__doc__)
p.add_option("--gauge_step", default=10000000, type="int",
help="Step size for the base scale")
opts, args, iopts = p.set_image_options(args, figsize="10x6")
if len(args) != 4:
sys.exit(not p.print_help())
chrs, sizes, bedfile, datadir = args
gauge_step = opts.gauge_step
chrs = [[x] for x in chrs.split(",")]
sizes = Sizes(sizes).mapping
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
chr_sizes, chr_sum_sizes, ratio = calc_ratio(chrs, sizes)
# Synteny panel
seqidsfile = make_seqids(chrs)
klayout = make_layout(chrs, chr_sum_sizes, ratio, template_f3a)
height = .11
r = height / 4
K = Karyotype(fig, root, seqidsfile, klayout, gap=gap,
height=height, lw=2, generank=False, sizes=sizes,
heightpad=r, roundrect=True)
# Inset with datafiles
datafiles = ("chrA02.bzh.forxmgr", "parent.A02.per10kb.forxmgr",
"parent.C2.per10kb.forxmgr", "chrC02.bzh.forxmgr")
datafiles = [op.join(datadir, x) for x in datafiles]
tracks = K.tracks
hlfile = op.join(datadir, "bzh.regions.forhaibao")
for t, datafile in zip(tracks, datafiles):
ax = make_affix_axis(fig, t, -r, height=2 * r)
chr = t.seqids[0]
xy = XYtrack(ax, datafile, color="lightslategray")
start, end = 0, t.total
xy.interpolate(end)
xy.cap(ymax=40)
xy.import_hlfile(hlfile, chr)
xy.draw()
ax.set_xlim(start, end)
gauge_ax = make_affix_axis(fig, t, -r)
adjust_spines(gauge_ax, ["bottom"])
setup_gauge_ax(gauge_ax, start, end, gauge_step)
# Converted gene tracks
ax_Ar = make_affix_axis(fig, tracks[1], r, height=r/2)
ax_Co = make_affix_axis(fig, tracks[2], r, height=r/2)
order = Bed(bedfile).order
for asterisk in (False, True):
conversion_track(order, "data/Genes.Converted.seuil.0.6.AtoC.txt",
0, "A02", ax_Ar, "r", asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.AtoC.txt",
1, "C2", ax_Co, "g", asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.CtoA.txt",
0, "A02", ax_Ar, "g", ypos=1, asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.CtoA.txt",
1, "C2", ax_Co, "r", ypos=1, asterisk=asterisk)
ax_Ar.set_xlim(0, tracks[1].total)
ax_Ar.set_ylim(-.5, 1.5)
ax_Co.set_xlim(0, tracks[2].total)
ax_Co.set_ylim(-.5, 1.5)
# Conversion legend
if False:
root.text(.81, .8, r"Converted A$\mathsf{_n}$ to C$\mathsf{_n}$",
va="center")
root.text(.81, .77, r"Converted C$\mathsf{_n}$ to A$\mathsf{_n}$",
va="center")
root.scatter([.8], [.8], s=20, color="g")
root.scatter([.8], [.77], s=20, color="r")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = "napusf3a." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def fig3(args):
"""
%prog fig3 chrA02,A02,C2,chrC02 chr.sizes all.bed data
Napus Figure 3 displays alignments between quartet chromosomes, inset
with read histograms.
"""
from jcvi.formats.bed import Bed
p = OptionParser(fig3.__doc__)
p.add_option("--gauge_step",
default=10000000,
type="int",
help="Step size for the base scale")
opts, args, iopts = p.set_image_options(args, figsize="12x9")
if len(args) != 4:
sys.exit(not p.print_help())
chrs, sizes, bedfile, datadir = args
gauge_step = opts.gauge_step
diverge = iopts.diverge
rr, gg = diverge
chrs = [[x] for x in chrs.split(",")]
sizes = Sizes(sizes).mapping
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
chr_sizes, chr_sum_sizes, ratio = calc_ratio(chrs, sizes)
# Synteny panel
seqidsfile = make_seqids(chrs)
klayout = make_layout(chrs, chr_sum_sizes, ratio, template_f3a, shift=.05)
height = .07
r = height / 4
K = Karyotype(fig,
root,
seqidsfile,
klayout,
gap=gap,
height=height,
lw=2,
generank=False,
sizes=sizes,
heightpad=r,
roundrect=True,
plot_label=False)
# Chromosome labels
for kl in K.layout:
if kl.empty:
continue
lx, ly = kl.xstart, kl.y
if lx < .11:
lx += .1
ly += .06
label = kl.label
root.text(lx - .015, ly, label, fontsize=15, ha="right", va="center")
# Inset with datafiles
datafiles = ("chrA02.bzh.forxmgr", "parent.A02.per10kb.forxmgr",
"parent.C2.per10kb.forxmgr", "chrC02.bzh.forxmgr")
datafiles = [op.join(datadir, x) for x in datafiles]
tracks = K.tracks
hlfile = op.join(datadir, "bzh.regions.forhaibao")
xy_axes = []
for t, datafile in zip(tracks, datafiles):
ax = make_affix_axis(fig, t, -r, height=2 * r)
xy_axes.append(ax)
chr = t.seqids[0]
xy = XYtrack(ax, datafile, color="lightslategray")
start, end = 0, t.total
xy.interpolate(end)
xy.cap(ymax=40)
xy.import_hlfile(hlfile, chr, diverge=diverge)
xy.draw()
ax.set_xlim(start, end)
gauge_ax = make_affix_axis(fig, t, -r)
adjust_spines(gauge_ax, ["bottom"])
setup_gauge_ax(gauge_ax, start, end, gauge_step)
# Converted gene tracks
ax_Ar = make_affix_axis(fig, tracks[1], r, height=r / 2)
ax_Co = make_affix_axis(fig, tracks[2], r, height=r / 2)
order = Bed(bedfile).order
for asterisk in (False, True):
conversion_track(order,
"data/Genes.Converted.seuil.0.6.AtoC.txt",
0,
"A02",
ax_Ar,
rr,
asterisk=asterisk)
conversion_track(order,
"data/Genes.Converted.seuil.0.6.AtoC.txt",
1,
"C2",
ax_Co,
gg,
asterisk=asterisk)
conversion_track(order,
"data/Genes.Converted.seuil.0.6.CtoA.txt",
0,
"A02",
ax_Ar,
gg,
ypos=1,
asterisk=asterisk)
conversion_track(order,
"data/Genes.Converted.seuil.0.6.CtoA.txt",
1,
"C2",
ax_Co,
rr,
ypos=1,
asterisk=asterisk)
Ar, Co = xy_axes[1:3]
annotations = ((Ar, "Bra028920 Bra028897", "center",
"1DAn2+"), (Ar, "Bra020081 Bra020171", "right", "2DAn2+"),
(Ar, "Bra020218 Bra020286", "left",
"3DAn2+"), (Ar, "Bra008143 Bra008167", "left", "4DAn2-"),
(Ar, "Bra029317 Bra029251", "right",
"5DAn2+ (GSL)"), (Co, "Bo2g001000 Bo2g001300", "left",
"1DCn2-"), (Co, "Bo2g018560 Bo2g023700",
"right", "2DCn2-"),
(Co, "Bo2g024450 Bo2g025390", "left",
"3DCn2-"), (Co, "Bo2g081060 Bo2g082340", "left", "4DCn2+"),
(Co, "Bo2g161510 Bo2g164260", "right", "5DCn2-"))
for ax, genes, ha, label in annotations:
g1, g2 = genes.split()
x1, x2 = order[g1][1].start, order[g2][1].start
if ha == "center":
x = (x1 + x2) / 2 * .8
elif ha == "left":
x = x2
else:
x = x1
label = r"\textit{{{0}}}".format(label)
color = rr if "+" in label else gg
ax.text(x, 30, label, color=color, fontsize=9, ha=ha, va="center")
ax_Ar.set_xlim(0, tracks[1].total)
ax_Ar.set_ylim(-1, 1)
ax_Co.set_xlim(0, tracks[2].total)
ax_Co.set_ylim(-1, 1)
# Plot coverage in resequencing lines
gstep = 5000000
order = "swede,kale,h165,yudal,aviso,abu,bristol".split(",")
labels_dict = {"h165": "Resynthesized (H165)", "abu": "Aburamasari"}
hlsuffix = "regions.forhaibao"
chr1, chr2 = "chrA02", "chrC02"
t1, t2 = tracks[0], tracks[-1]
s1, s2 = sizes[chr1], sizes[chr2]
canvas1 = (t1.xstart, .75, t1.xend - t1.xstart, .2)
c = Coverage(fig,
root,
canvas1,
chr1, (0, s1),
datadir,
order=order,
gauge=None,
plot_chr_label=False,
gauge_step=gstep,
palette="gray",
cap=40,
hlsuffix=hlsuffix,
labels_dict=labels_dict,
diverge=diverge)
yys = c.yys
x1, x2 = .37, .72
tip = .02
annotations = ((x1, yys[2] + .3 * tip, tip, tip / 2,
"FLC"), (x1, yys[3] + .6 * tip, tip, tip / 2, "FLC"),
(x1, yys[5] + .6 * tip, tip, tip / 2,
"FLC"), (x2, yys[0] + .9 * tip, -1.2 * tip, 0, "GSL"),
(x2, yys[4] + .9 * tip, -1.2 * tip, 0,
"GSL"), (x2, yys[6] + .9 * tip, -1.2 * tip, 0, "GSL"))
arrowprops = dict(facecolor='black',
shrink=.05,
frac=.5,
width=1,
headwidth=4)
for x, y, dx, dy, label in annotations:
label = r"\textit{{{0}}}".format(label)
root.annotate(label,
xy=(x, y),
xytext=(x + dx, y + dy),
arrowprops=arrowprops,
color=rr,
fontsize=9,
ha="center",
va="center")
canvas2 = (t2.xstart, .05, t2.xend - t2.xstart, .2)
Coverage(fig,
root,
canvas2,
chr2, (0, s2),
datadir,
order=order,
gauge=None,
plot_chr_label=False,
gauge_step=gstep,
palette="gray",
cap=40,
hlsuffix=hlsuffix,
labels_dict=labels_dict,
diverge=diverge)
pad = .03
labels = ((.1, .67, "A"), (t1.xstart - 3 * pad, .95 + pad, "B"),
(t2.xstart - 3 * pad, .25 + pad, "C"))
panel_labels(root, labels)
normalize_axes(root)
image_name = "napus-fig3." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def fig3(args):
"""
%prog fig3 chrA02,A02,C2,chrC02 chr.sizes all.bed data
Napus Figure 3 displays alignments between quartet chromosomes, inset
with read histograms.
"""
from jcvi.formats.bed import Bed
p = OptionParser(fig3.__doc__)
p.add_option("--gauge_step", default=10000000, type="int",
help="Step size for the base scale")
opts, args, iopts = p.set_image_options(args, figsize="12x9")
if len(args) != 4:
sys.exit(not p.print_help())
chrs, sizes, bedfile, datadir = args
gauge_step = opts.gauge_step
diverge = iopts.diverge
rr, gg = diverge
chrs = [[x] for x in chrs.split(",")]
sizes = Sizes(sizes).mapping
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
chr_sizes, chr_sum_sizes, ratio = calc_ratio(chrs, sizes)
# Synteny panel
seqidsfile = make_seqids(chrs)
klayout = make_layout(chrs, chr_sum_sizes, ratio, template_f3a, shift=.05)
height = .07
r = height / 4
K = Karyotype(fig, root, seqidsfile, klayout, gap=gap,
height=height, lw=2, generank=False, sizes=sizes,
heightpad=r, roundrect=True, plot_label=False)
# Chromosome labels
for kl in K.layout:
if kl.empty:
continue
lx, ly = kl.xstart, kl.y
if lx < .11:
lx += .1
ly += .06
label = kl.label
root.text(lx - .015, ly, label, fontsize=15,
ha="right", va="center")
# Inset with datafiles
datafiles = ("chrA02.bzh.forxmgr", "parent.A02.per10kb.forxmgr",
"parent.C2.per10kb.forxmgr", "chrC02.bzh.forxmgr")
datafiles = [op.join(datadir, x) for x in datafiles]
tracks = K.tracks
hlfile = op.join(datadir, "bzh.regions.forhaibao")
xy_axes = []
for t, datafile in zip(tracks, datafiles):
ax = make_affix_axis(fig, t, -r, height=2 * r)
xy_axes.append(ax)
chr = t.seqids[0]
xy = XYtrack(ax, datafile, color="lightslategray")
start, end = 0, t.total
xy.interpolate(end)
xy.cap(ymax=40)
xy.import_hlfile(hlfile, chr, diverge=diverge)
xy.draw()
ax.set_xlim(start, end)
gauge_ax = make_affix_axis(fig, t, -r)
adjust_spines(gauge_ax, ["bottom"])
setup_gauge_ax(gauge_ax, start, end, gauge_step)
# Converted gene tracks
ax_Ar = make_affix_axis(fig, tracks[1], r, height=r/2)
ax_Co = make_affix_axis(fig, tracks[2], r, height=r/2)
order = Bed(bedfile).order
for asterisk in (False, True):
conversion_track(order, "data/Genes.Converted.seuil.0.6.AtoC.txt",
0, "A02", ax_Ar, rr, asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.AtoC.txt",
1, "C2", ax_Co, gg, asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.CtoA.txt",
0, "A02", ax_Ar, gg, ypos=1, asterisk=asterisk)
conversion_track(order, "data/Genes.Converted.seuil.0.6.CtoA.txt",
1, "C2", ax_Co, rr, ypos=1, asterisk=asterisk)
Ar, Co = xy_axes[1:3]
annotations = ((Ar, "Bra028920 Bra028897", "center", "1DAn2+"),
(Ar, "Bra020081 Bra020171", "right", "2DAn2+"),
(Ar, "Bra020218 Bra020286", "left", "3DAn2+"),
(Ar, "Bra008143 Bra008167", "left", "4DAn2-"),
(Ar, "Bra029317 Bra029251", "right", "5DAn2+ (GSL)"),
(Co, "Bo2g001000 Bo2g001300", "left", "1DCn2-"),
(Co, "Bo2g018560 Bo2g023700", "right", "2DCn2-"),
(Co, "Bo2g024450 Bo2g025390", "left", "3DCn2-"),
(Co, "Bo2g081060 Bo2g082340", "left", "4DCn2+"),
(Co, "Bo2g161510 Bo2g164260", "right", "5DCn2-"))
for ax, genes, ha, label in annotations:
g1, g2 = genes.split()
x1, x2 = order[g1][1].start, order[g2][1].start
if ha == "center":
x = (x1 + x2) / 2 * .8
elif ha == "left":
x = x2
else:
x = x1
label = r"\textit{{{0}}}".format(label)
color = rr if "+" in label else gg
ax.text(x, 30, label, color=color, fontsize=9, ha=ha, va="center")
ax_Ar.set_xlim(0, tracks[1].total)
ax_Ar.set_ylim(-1, 1)
ax_Co.set_xlim(0, tracks[2].total)
ax_Co.set_ylim(-1, 1)
# Plot coverage in resequencing lines
gstep = 5000000
order = "swede,kale,h165,yudal,aviso,abu,bristol".split(",")
labels_dict = {"h165": "Resynthesized (H165)", "abu": "Aburamasari"}
hlsuffix = "regions.forhaibao"
chr1, chr2 = "chrA02", "chrC02"
t1, t2 = tracks[0], tracks[-1]
s1, s2 = sizes[chr1], sizes[chr2]
canvas1 = (t1.xstart, .75, t1.xend - t1.xstart, .2)
c = Coverage(fig, root, canvas1, chr1, (0, s1), datadir,
order=order, gauge=None, plot_chr_label=False,
gauge_step=gstep, palette="gray",
cap=40, hlsuffix=hlsuffix, labels_dict=labels_dict,
diverge=diverge)
yys = c.yys
x1, x2 = .37, .72
tip = .02
annotations = ((x1, yys[2] + .3 * tip, tip, tip / 2, "FLC"),
(x1, yys[3] + .6 * tip, tip, tip / 2, "FLC"),
(x1, yys[5] + .6 * tip, tip, tip / 2, "FLC"),
(x2, yys[0] + .9 * tip, -1.2 * tip, 0, "GSL"),
(x2, yys[4] + .9 * tip, -1.2 * tip, 0, "GSL"),
(x2, yys[6] + .9 * tip, -1.2 * tip, 0, "GSL"))
arrowprops=dict(facecolor='black', shrink=.05, frac=.5,
width=1, headwidth=4)
for x, y, dx, dy, label in annotations:
label = r"\textit{{{0}}}".format(label)
root.annotate(label, xy=(x, y), xytext=(x + dx, y + dy),
arrowprops=arrowprops, color=rr, fontsize=9,
ha="center", va="center")
canvas2 = (t2.xstart, .05, t2.xend - t2.xstart, .2)
Coverage(fig, root, canvas2, chr2, (0, s2), datadir,
order=order, gauge=None, plot_chr_label=False,
gauge_step=gstep, palette="gray",
cap=40, hlsuffix=hlsuffix, labels_dict=labels_dict,
diverge=diverge)
pad = .03
labels = ((.1, .67, "A"), (t1.xstart - 3 * pad, .95 + pad, "B"),
(t2.xstart - 3 * pad, .25 + pad, "C"))
panel_labels(root, labels)
normalize_axes(root)
image_name = "napus-fig3." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)