def scaffold(args):
"""
%prog scaffold scaffold.fasta synteny.blast synteny.sizes synteny.bed
physicalmap.blast physicalmap.sizes physicalmap.bed
As evaluation of scaffolding, visualize external line of evidences:
* Plot synteny to an external genome
* Plot alignments to physical map
* Plot alignments to genetic map (TODO)
Each trio defines one panel to be plotted. blastfile defines the matchings
between the evidences vs scaffolds. Then the evidence sizes, and evidence
bed to plot dot plots.
This script will plot a dot in the dot plot in the corresponding location
the plots are one contig/scaffold per plot.
"""
from jcvi.graphics.base import set_image_options
from jcvi.utils.iter import grouper
p = OptionParser(scaffold.__doc__)
p.add_option("--cutoff", type="int", default=1000000,
help="Plot scaffolds with size larger than [default: %default]")
p.add_option("--highlights",
help="A set of regions in BED format to highlight [default: %default]")
opts, args, iopts = set_image_options(p, args, figsize="14x8", dpi=150)
if len(args) < 4 or len(args) % 3 != 1:
sys.exit(not p.print_help())
highlights = opts.highlights
scafsizes = Sizes(args[0])
trios = list(grouper(3, args[1:]))
trios = [(a, Sizes(b), Bed(c)) for a, b, c in trios]
if highlights:
hlbed = Bed(highlights)
for scaffoldID, scafsize in scafsizes.iter_sizes():
if scafsize < opts.cutoff:
continue
logging.debug("Loading {0} (size={1})".format(scaffoldID,
thousands(scafsize)))
tmpname = scaffoldID + ".sizes"
tmp = open(tmpname, "w")
tmp.write("{0}\t{1}".format(scaffoldID, scafsize))
tmp.close()
tmpsizes = Sizes(tmpname)
tmpsizes.close(clean=True)
if highlights:
subhighlights = list(hlbed.sub_bed(scaffoldID))
imagename = ".".join((scaffoldID, opts.format))
plot_one_scaffold(scaffoldID, tmpsizes, None, trios, imagename, iopts,
highlights=subhighlights)
def main():
"""
%prog bedfile id_mappings
Takes a bedfile that contains the coordinates of features to plot on the
chromosomes, and `id_mappings` file that map the ids to certain class. Each
class will get assigned a unique color. `id_mappings` file is optional (if
omitted, will not paint the chromosome features, except the centromere).
"""
p = OptionParser(main.__doc__)
p.add_option("--title",
default="Medicago truncatula v3.5",
help="title of the image [default: `%default`]")
p.add_option("--gauge",
default=False,
action="store_true",
help="draw a gauge with size label [default: %default]")
p.add_option(
"--imagemap",
default=False,
action="store_true",
help=
"generate an HTML image map associated with the image [default: %default]"
)
p.add_option(
"--winsize",
default=50000,
type="int",
help=
"if drawing an imagemap, specify the window size (bases) of each map element "
"[default: %default bp]")
p.add_option("--empty", help="Write legend for unpainted region")
opts, args, iopts = p.set_image_options(figsize="6x6", dpi=300)
if len(args) not in (1, 2):
sys.exit(p.print_help())
bedfile = args[0]
mappingfile = None
if len(args) == 2:
mappingfile = args[1]
winsize = opts.winsize
imagemap = opts.imagemap
w, h = iopts.w, iopts.h
dpi = iopts.dpi
prefix = bedfile.rsplit(".", 1)[0]
figname = prefix + "." + opts.format
if imagemap:
imgmapfile = prefix + '.map'
mapfh = open(imgmapfile, "w")
print >> mapfh, '<map id="' + prefix + '">'
if mappingfile:
mappings = DictFile(mappingfile, delimiter="\t")
classes = sorted(set(mappings.values()))
logging.debug("A total of {0} classes found: {1}".format(
len(classes), ','.join(classes)))
else:
mappings = {}
classes = []
logging.debug("No classes registered (no id_mappings given).")
mycolors = "rgbymc"
class_colors = dict(zip(classes, mycolors))
bed = Bed(bedfile)
chr_lens = {}
centromeres = {}
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)
assert chr_number == len(centromeres)
fig = plt.figure(1, (w, h))
root = fig.add_axes([0, 0, 1, 1])
r = .7 # width and height of the whole chromosome set
xstart, ystart = .15, .85
xinterval = r / chr_number
xwidth = xinterval * .5 # chromosome width
max_chr_len = max(chr_lens.values())
ratio = r / max_chr_len # canvas / base
# first the chromosomes
for a, (chr, cent_position) in enumerate(sorted(centromeres.items())):
clen = chr_lens[chr]
xx = xstart + a * xinterval + .5 * xwidth
yy = ystart - cent_position * ratio
root.text(xx, ystart + .01, chr, ha="center")
ChromosomeWithCentromere(root,
xx,
ystart,
yy,
ystart - clen * ratio,
width=xwidth)
chr_idxs = dict((a, i) for i, a in enumerate(sorted(chr_lens.keys())))
alpha = .75
# color the regions
for chr in sorted(chr_lens.keys()):
segment_size, excess = 0, 0
bac_list = []
for b in bed.sub_bed(chr):
clen = chr_lens[chr]
idx = chr_idxs[chr]
klass = b.accn
start = b.start
end = b.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, "w"),
lw=0,
alpha=alpha))
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 >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)
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 >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)
if imagemap:
print >> mapfh, '</map>'
mapfh.close()
logging.debug("Image map written to `{0}`".format(mapfh.name))
if opts.gauge:
xstart, ystart = .9, .85
Gauge(root, xstart, ystart - r, ystart, max_chr_len)
# class legends, four in a row
xstart = .1
xinterval = .2
xwidth = .04
yy = .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 + .01, yy, klass, fontsize=10)
xstart += xinterval
empty = opts.empty
if empty:
root.add_patch(
Rectangle((xstart, yy), xwidth, xwidth, fill=False, lw=1))
root.text(xstart + xwidth + .01, yy, empty, fontsize=10)
root.text(.5,
.95,
opts.title,
fontstyle="italic",
ha="center",
va="center")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
savefig(figname, dpi=dpi, iopts=iopts)
def plot(args):
"""
%prog plot tagged.new.bed chr1
Plot gene identifiers along a particular chromosome, often to illustrate the
gene id assignment procedure.
"""
from jcvi.graphics.base import plt, savefig
from jcvi.graphics.chromosome import ChromosomeMap
p = OptionParser(plot.__doc__)
p.add_option("--firstn", type="int", help="Only plot the first N genes")
p.add_option("--ymax", type="int", help="Y-axis max value")
p.add_option("--log",
action="store_true",
help="Write plotting data [default: %default]")
opts, args, iopts = p.set_image_options(args, figsize="6x4")
if len(args) != 2:
sys.exit(not p.print_help())
taggedbed, chr = args
bed = Bed(taggedbed)
beds = list(bed.sub_bed(chr))
old, new = [], []
i = 0
for b in beds:
accn = b.extra[0]
if "te" in accn:
continue
accn, tag = accn.split("|")
if tag == "OVERLAP":
continue
c, r = atg_name(accn)
if tag == "NEW":
new.append((i, r))
else:
old.append((i, r))
i += 1
ngenes = i
assert ngenes == len(new) + len(old)
logging.debug("Imported {0} ranks on {1}.".format(ngenes, chr))
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
xstart, xend = .2, .8
ystart, yend = .2, .8
pad = .02
ngenes = opts.firstn or ngenes
ymax = opts.ymax or 500000
title = "Assignment of Medtr identifiers"
if opts.ymax:
subtitle = "{0}, first {1} genes".format(chr, ngenes)
else:
subtitle = "{0}, {1} genes ({2} new)".format(chr, ngenes, len(new))
chr_map = ChromosomeMap(fig, root, xstart, xend, ystart, yend, pad, 0,
ymax, 5, title, subtitle)
ax = chr_map.axes
if opts.log:
from jcvi.utils.table import write_csv
header = ["x", "y"]
write_csv(header, new, filename=chr + ".new")
write_csv(header, old, filename=chr + ".old")
x, y = zip(*new)
ax.plot(x, y, "b,")
x, y = zip(*old)
ax.plot(x, y, "r,")
# Legends
ymid = (ystart + yend) / 2
y = ymid + pad
root.plot([.2], [y], "r.", lw=2)
root.text(.2 + pad, y, "Existing Medtr ids", va="center", size=10)
y = ymid - pad
root.plot([.2], [y], "b.", lw=2)
root.text(.2 + pad, y, "Newly instantiated ids", va="center", size=10)
ax.set_xlim(0, ngenes)
ax.set_ylim(0, ymax)
ax.set_axis_off()
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + ".identifiers." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def plot(args):
"""
%prog plot tagged.new.bed chr1
Plot gene identifiers along a particular chromosome, often to illustrate the
gene id assignment procedure.
"""
from jcvi.graphics.base import plt, savefig
from jcvi.graphics.chromosome import ChromosomeMap
p = OptionParser(plot.__doc__)
p.add_option("--firstn", type="int", help="Only plot the first N genes")
p.add_option("--ymax", type="int", help="Y-axis max value")
p.add_option("--log", action="store_true",
help="Write plotting data [default: %default]")
opts, args, iopts = p.set_image_options(args, figsize="6x4")
if len(args) != 2:
sys.exit(not p.print_help())
taggedbed, chr = args
bed = Bed(taggedbed)
beds = list(bed.sub_bed(chr))
old, new = [], []
i = 0
for b in beds:
accn = b.extra[0]
if "te" in accn:
continue
accn, tag = accn.split("|")
if tag == "OVERLAP":
continue
c, r = atg_name(accn)
if tag == "NEW":
new.append((i, r))
else:
old.append((i, r))
i += 1
ngenes = i
assert ngenes == len(new) + len(old)
logging.debug("Imported {0} ranks on {1}.".format(ngenes, chr))
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
xstart, xend = .2, .8
ystart, yend = .2, .8
pad = .02
ngenes = opts.firstn or ngenes
ymax = opts.ymax or 500000
title = "Assignment of Medtr identifiers"
if opts.ymax:
subtitle = "{0}, first {1} genes".format(chr, ngenes)
else:
subtitle = "{0}, {1} genes ({2} new)".format(chr, ngenes, len(new))
chr_map = ChromosomeMap(fig, root, xstart, xend, ystart, yend, pad, 0,
ymax, 5, title, subtitle)
ax = chr_map.axes
if opts.log:
from jcvi.utils.table import write_csv
header = ["x", "y"]
write_csv(header, new, filename=chr + ".new")
write_csv(header, old, filename=chr + ".old")
x, y = zip(*new)
ax.plot(x, y, "b,")
x, y = zip(*old)
ax.plot(x, y, "r,")
# Legends
ymid = (ystart + yend) / 2
y = ymid + pad
root.plot([.2], [y], "r.", lw=2)
root.text(.2 + pad, y, "Existing Medtr ids", va="center", size=10)
y = ymid - pad
root.plot([.2], [y], "b.", lw=2)
root.text(.2 + pad, y, "Newly instantiated ids", va="center", size=10)
ax.set_xlim(0, ngenes)
ax.set_ylim(0, ymax)
ax.set_axis_off()
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + ".identifiers." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def main():
"""
%prog bedfile id_mappings
Takes a bedfile that contains the coordinates of features to plot on the
chromosomes, and `id_mappings` file that map the ids to certain class. Each
class will get assigned a unique color. `id_mappings` file is optional (if
omitted, will not paint the chromosome features, except the centromere).
"""
p = OptionParser(main.__doc__)
p.add_option("--title", default="Medicago truncatula v3.5",
help="title of the image [default: `%default`]")
p.add_option("--gauge", default=False, action="store_true",
help="draw a gauge with size label [default: %default]")
p.add_option("--imagemap", default=False, action="store_true",
help="generate an HTML image map associated with the image [default: %default]")
p.add_option("--winsize", default=50000, type="int",
help="if drawing an imagemap, specify the window size (bases) of each map element "
"[default: %default bp]")
opts, args, iopts = set_image_options(p, figsize="6x6", dpi=300)
if len(args) not in (1, 2):
sys.exit(p.print_help())
bedfile = args[0]
mappingfile = None
if len(args) == 2:
mappingfile = args[1]
winsize = opts.winsize
imagemap = opts.imagemap
w, h = iopts.w, iopts.h
dpi = iopts.dpi
prefix = bedfile.rsplit(".", 1)[0]
figname = prefix + "." + opts.format
if imagemap:
imgmapfile = prefix + '.map'
mapfh = open(imgmapfile, "w")
print >> mapfh, '<map id="' + prefix + '">'
if mappingfile:
mappings = dict(x.split() for x in open(mappingfile))
classes = sorted(set(mappings.values()))
logging.debug("A total of {0} classes found: {1}".format(len(classes),
','.join(classes)))
else:
mappings = {}
classes = []
logging.debug("No classes registered (no id_mappings given).")
mycolors = "wrgbymc"
class_colors = dict(zip(classes, mycolors))
bed = Bed(bedfile)
chr_lens = {}
centromeres = {}
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)
assert chr_number == len(centromeres)
fig = plt.figure(1, (w, h))
root = fig.add_axes([0, 0, 1, 1])
r = .7 # width and height of the whole chromosome set
xstart, ystart = .15, .85
xinterval = r / chr_number
xwidth = xinterval * .5 # chromosome width
max_chr_len = max(chr_lens.values())
ratio = r / max_chr_len # canvas / base
# first the chromosomes
for a, (chr, cent_position) in enumerate(sorted(centromeres.items())):
clen = chr_lens[chr]
xx = xstart + a * xinterval + .5 * xwidth
yy = ystart - cent_position * ratio
root.text(xx, ystart + .01, _(chr), ha="center")
ChromosomeWithCentromere(root, xx, ystart, yy,
ystart - clen * ratio, width=xwidth)
chr_idxs = dict((a, i) for i, a in enumerate(sorted(chr_lens.keys())))
alpha = .75
# color the regions
for chr in sorted(chr_lens.keys()):
segment_size, excess = 0, 0
bac_list = []
for b in bed.sub_bed(chr):
clen = chr_lens[chr]
idx = chr_idxs[chr]
klass = b.accn
start = b.start
end = b.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, "w"), lw=0, alpha=alpha))
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 >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)
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 >> mapfh, '\t' + write_ImageMapLine(tlx, tly, brx, bry, \
w, h, dpi, chr+":"+",".join(bac_list), segment_start, segment_end)
if imagemap:
print >> mapfh, '</map>'
mapfh.close()
logging.debug("Image map written to `{0}`".format(mapfh.name))
if opts.gauge:
tip = .008 # the ticks on the gauge bar
extra = .006 # the offset for the unit label
xstart, ystart = .9, .85
yy = ystart
gauge = int(ceil(max_chr_len / 1e6))
mb = ratio * 1e6
yinterval = 2 * mb
root.plot([xstart, xstart], [yy, yy - r], 'b-', lw=2)
for x in xrange(0, gauge, 2):
if x % 10:
root.plot([xstart, xstart + tip], [yy, yy], "b-")
else:
root.plot([xstart - tip, xstart + tip], [yy, yy], 'b-', lw=2)
root.text(xstart + tip + extra, yy, _(x),
color="gray", va="center")
yy -= yinterval
root.text(xstart, yy - .03, _("Mb"), color="gray", va="center")
# class legends, four in a row
xstart = .1
xinterval = .2
xwidth = .04
yy = .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 + .01, yy, _(klass), fontsize=9)
xstart += xinterval
root.text(.5, .95, opts.title, fontstyle="italic", ha="center", va="center")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
plt.savefig(figname, dpi=dpi)
logging.debug("Figure saved to `{0}` {1}".format(figname, iopts))
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")
