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")
