def draw_chromosomes(
root,
bedfile,
sizes,
iopts,
mergedist,
winsize,
imagemap,
mappingfile=None,
gauge=False,
legend=True,
empty=False,
title=None,
):
bed = Bed(bedfile)
prefix = bedfile.rsplit(".", 1)[0]
if imagemap:
imgmapfile = prefix + ".map"
mapfh = open(imgmapfile, "w")
print('<map id="' + prefix + '">', file=mapfh)
if mappingfile:
mappings = DictFile(mappingfile, delimiter="\t")
classes = sorted(set(mappings.values()))
preset_colors = (DictFile(
mappingfile, keypos=1, valuepos=2, delimiter="\t")
if DictFile.num_columns(mappingfile) >= 3 else {})
else:
classes = sorted(set(x.accn for x in bed))
mappings = dict((x, x) for x in classes)
preset_colors = {}
logging.debug("A total of {} classes found: {}".format(
len(classes), ",".join(classes)))
# Assign colors to classes
ncolors = max(3, min(len(classes), 12))
palette = set1_n if ncolors <= 8 else set3_n
colorset = palette(number=ncolors)
colorset = sample_N(colorset, len(classes))
class_colors = dict(zip(classes, colorset))
class_colors.update(preset_colors)
logging.debug("Assigned colors: {}".format(class_colors))
chr_lens = {}
centromeres = {}
if sizes:
chr_lens = Sizes(sizes).sizes_mapping
else:
for b, blines in groupby(bed, key=(lambda x: x.seqid)):
blines = list(blines)
maxlen = max(x.end for x in blines)
chr_lens[b] = maxlen
for b in bed:
accn = b.accn
if accn == "centromere":
centromeres[b.seqid] = b.start
if accn in mappings:
b.accn = mappings[accn]
else:
b.accn = "-"
chr_number = len(chr_lens)
if centromeres:
assert chr_number == len(
centromeres), "chr_number = {}, centromeres = {}".format(
chr_number, centromeres)
r = 0.7 # width and height of the whole chromosome set
xstart, ystart = 0.15, 0.85
xinterval = r / chr_number
xwidth = xinterval * 0.5 # chromosome width
max_chr_len = max(chr_lens.values())
ratio = r / max_chr_len # canvas / base
# first the chromosomes
for a, (chr, clen) in enumerate(sorted(chr_lens.items())):
xx = xstart + a * xinterval + 0.5 * xwidth
root.text(xx, ystart + 0.01, str(get_number(chr)), ha="center")
if centromeres:
yy = ystart - centromeres[chr] * ratio
ChromosomeWithCentromere(root,
xx,
ystart,
yy,
ystart - clen * ratio,
width=xwidth)
else:
Chromosome(root, xx, ystart, ystart - clen * ratio, width=xwidth)
chr_idxs = dict((a, i) for i, a in enumerate(sorted(chr_lens.keys())))
alpha = 1
# color the regions
for chr in sorted(chr_lens.keys()):
segment_size, excess = 0, 0
bac_list = []
prev_end, prev_klass = 0, None
for b in bed.sub_bed(chr):
clen = chr_lens[chr]
idx = chr_idxs[chr]
klass = b.accn
if klass == "centromere":
continue
start = b.start
end = b.end
if start < prev_end + mergedist and klass == prev_klass:
start = prev_end
xx = xstart + idx * xinterval
yystart = ystart - end * ratio
yyend = ystart - start * ratio
root.add_patch(
Rectangle(
(xx, yystart),
xwidth,
yyend - yystart,
fc=class_colors.get(klass, "lightslategray"),
lw=0,
alpha=alpha,
))
prev_end, prev_klass = b.end, klass
if imagemap:
"""
`segment` : size of current BAC being investigated + `excess`
`excess` : left-over bases from the previous BAC, as a result of
iterating over `winsize` regions of `segment`
"""
if excess == 0:
segment_start = start
segment = (end - start + 1) + excess
while True:
if segment < winsize:
bac_list.append(b.accn)
excess = segment
break
segment_end = segment_start + winsize - 1
tlx, tly, brx, bry = (
xx,
(1 - ystart) + segment_start * ratio,
xx + xwidth,
(1 - ystart) + segment_end * ratio,
)
print(
"\t" + write_ImageMapLine(
tlx,
tly,
brx,
bry,
iopts.w,
iopts.h,
iopts.dpi,
chr + ":" + ",".join(bac_list),
segment_start,
segment_end,
),
file=mapfh,
)
segment_start += winsize
segment -= winsize
bac_list = []
if imagemap and excess > 0:
bac_list.append(b.accn)
segment_end = end
tlx, tly, brx, bry = (
xx,
(1 - ystart) + segment_start * ratio,
xx + xwidth,
(1 - ystart) + segment_end * ratio,
)
print(
"\t" + write_ImageMapLine(
tlx,
tly,
brx,
bry,
iopts.w,
iopts.h,
iopts.dpi,
chr + ":" + ",".join(bac_list),
segment_start,
segment_end,
),
file=mapfh,
)
if imagemap:
print("</map>", file=mapfh)
mapfh.close()
logging.debug("Image map written to `{0}`".format(mapfh.name))
if gauge:
xstart, ystart = 0.9, 0.85
Gauge(root, xstart, ystart - r, ystart, max_chr_len)
if "centromere" in class_colors:
del class_colors["centromere"]
# class legends, four in a row
if legend:
xstart = 0.1
xinterval = 0.8 / len(class_colors)
xwidth = 0.04
yy = 0.08
for klass, cc in sorted(class_colors.items()):
if klass == "-":
continue
root.add_patch(
Rectangle((xstart, yy),
xwidth,
xwidth,
fc=cc,
lw=0,
alpha=alpha))
root.text(xstart + xwidth + 0.01, yy, latex(klass), fontsize=10)
xstart += xinterval
if empty:
root.add_patch(
Rectangle((xstart, yy), xwidth, xwidth, fill=False, lw=1))
root.text(xstart + xwidth + 0.01, yy, empty, fontsize=10)
if title:
root.text(0.5, 0.95, markup(title), ha="center", va="center")
def ancestral(args):
"""
%prog ancestral ancestral.txt assembly.fasta
Karyotype evolution of pineapple. The figure is inspired by Amphioxus paper
Figure 3 and Tetradon paper Figure 9.
"""
p = OptionParser(ancestral.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="8x7")
if len(args) != 2:
sys.exit(not p.print_help())
regionsfile, sizesfile = args
regions = RegionsFile(regionsfile)
sizes = Sizes(sizesfile).mapping
sizes = dict((k, v) for (k, v) in sizes.iteritems() if k[:2] == "LG")
maxsize = max(sizes.values())
ratio = .5 / maxsize
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes((0, 0, 1, 1))
from jcvi.graphics.base import set2
a, b, c, d, e, f, g = set2[:7]
set2 = (c, g, b, e, d, a, f)
# Upper panel is the evolution of segments
# All segments belong to one of seven karyotypes 1 to 7
karyotypes = regions.karyotypes
xgap = 1. / (1 + len(karyotypes))
ygap = .05
mgap = xgap / 4.5
gwidth = mgap * .75
tip = .02
coords = {}
for i, k in enumerate(regions.karyotypes):
x = (i + 1) * xgap
y = .9
root.text(x, y + tip, "Anc" + k, ha="center")
root.plot((x, x), (y, y - ygap), "k-", lw=2)
y -= 2 * ygap
coords['a'] = (x - 1.5 * mgap , y)
coords['b'] = (x - .5 * mgap , y)
coords['c'] = (x + .5 * mgap , y)
coords['d'] = (x + 1.5 * mgap , y)
coords['ab'] = join_nodes_vertical(root, coords, 'a', 'b', y + ygap / 2)
coords['cd'] = join_nodes_vertical(root, coords, 'c', 'd', y + ygap / 2)
coords['abcd'] = join_nodes_vertical(root, coords, 'ab', 'cd', y + ygap)
for n in 'abcd':
nx, ny = coords[n]
root.text(nx, ny - tip, n, ha="center")
coords[n] = (nx, ny - ygap / 2)
kdata = regions.get_karyotype(k)
for kd in kdata:
g = kd.group
gx, gy = coords[g]
gsize = ratio * kd.span
gy -= gsize
p = Rectangle((gx - gwidth / 2, gy),
gwidth, gsize, lw=0, color=set2[i])
root.add_patch(p)
root.text(gx, gy + gsize / 2, kd.chromosome,
ha="center", va="center", color='w')
coords[g] = (gx, gy - tip)
# Bottom panel shows the location of segments on chromosomes
# TODO: redundant code, similar to graphics.chromosome
ystart = .54
chr_number = len(sizes)
xstart, xend = xgap - 2 * mgap, 1 - xgap + 2 * mgap
xinterval = (xend - xstart - gwidth) / (chr_number - 1)
chrpos = {}
for a, (chr, clen) in enumerate(sorted(sizes.items())):
chr = get_number(chr)
xx = xstart + a * xinterval + gwidth / 2
chrpos[chr] = xx
root.text(xx, ystart + .01, chr, ha="center")
Chromosome(root, xx, ystart, ystart - clen * ratio, width=gwidth)
# Start painting
for r in regions:
xx = chrpos[r.chromosome]
yystart = ystart - r.start * ratio
yyend = ystart - r.end * ratio
p = Rectangle((xx - gwidth / 2, yystart), gwidth, yyend - yystart,
color=set2[int(r.karyotype) - 1], lw=0)
root.add_patch(p)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
pf = "pineapple-karyotype"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def ancestral(args):
"""
%prog ancestral ancestral.txt assembly.fasta
Karyotype evolution of pineapple. The figure is inspired by Amphioxus paper
Figure 3 and Tetradon paper Figure 9.
"""
p = OptionParser(ancestral.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="8x7")
if len(args) != 2:
sys.exit(not p.print_help())
regionsfile, sizesfile = args
regions = RegionsFile(regionsfile)
sizes = Sizes(sizesfile).mapping
sizes = dict((k, v) for (k, v) in sizes.iteritems() if k[:2] == "LG")
maxsize = max(sizes.values())
ratio = .5 / maxsize
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes((0, 0, 1, 1))
from jcvi.graphics.base import set2
a, b, c, d, e, f, g = set2[:7]
set2 = (c, g, b, e, d, a, f)
# Upper panel is the evolution of segments
# All segments belong to one of seven karyotypes 1 to 7
karyotypes = regions.karyotypes
xgap = 1. / (1 + len(karyotypes))
ygap = .05
mgap = xgap / 4.5
gwidth = mgap * .75
tip = .02
coords = {}
for i, k in enumerate(regions.karyotypes):
x = (i + 1) * xgap
y = .9
root.text(x, y + tip, "Anc" + k, ha="center")
root.plot((x, x), (y, y - ygap), "k-", lw=2)
y -= 2 * ygap
coords['a'] = (x - 1.5 * mgap , y)
coords['b'] = (x - .5 * mgap , y)
coords['c'] = (x + .5 * mgap , y)
coords['d'] = (x + 1.5 * mgap , y)
coords['ab'] = join_nodes_vertical(root, coords, 'a', 'b', y + ygap / 2)
coords['cd'] = join_nodes_vertical(root, coords, 'c', 'd', y + ygap / 2)
coords['abcd'] = join_nodes_vertical(root, coords, 'ab', 'cd', y + ygap)
for n in 'abcd':
nx, ny = coords[n]
root.text(nx, ny - tip, n, ha="center")
coords[n] = (nx, ny - ygap / 2)
kdata = regions.get_karyotype(k)
for kd in kdata:
g = kd.group
gx, gy = coords[g]
gsize = ratio * kd.span
gy -= gsize
p = Rectangle((gx - gwidth / 2, gy),
gwidth, gsize, lw=0, color=set2[i])
root.add_patch(p)
root.text(gx, gy + gsize / 2, kd.chromosome,
ha="center", va="center", color='w')
coords[g] = (gx, gy - tip)
# Bottom panel shows the location of segments on chromosomes
# TODO: redundant code, similar to graphics.chromosome
ystart = .54
chr_number = len(sizes)
xstart, xend = xgap - 2 * mgap, 1 - xgap + 2 * mgap
xinterval = (xend - xstart - gwidth) / (chr_number - 1)
chrpos = {}
for a, (chr, clen) in enumerate(sorted(sizes.items())):
chr = get_number(chr)
xx = xstart + a * xinterval + gwidth / 2
chrpos[chr] = xx
root.text(xx, ystart + .01, chr, ha="center")
Chromosome(root, xx, ystart, ystart - clen * ratio, width=gwidth)
# Start painting
for r in regions:
xx = chrpos[r.chromosome]
yystart = ystart - r.start * ratio
yyend = ystart - r.end * ratio
p = Rectangle((xx - gwidth / 2, yystart), gwidth, yyend - yystart,
color=set2[int(r.karyotype) - 1], lw=0)
root.add_patch(p)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
pf = "pineapple-karyotype"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
