def main(tx=None):
"""
%prog newicktree
Plot Newick formatted tree. The gene structure can be plotted along if
--gffdir is given. The gff file needs to be `genename.gff`. If --sizes is
on, also show the number of amino acids.
"""
p = OptionParser(main.__doc__)
p.add_option("--outgroup", help="Root the tree using the outgroup. " + \
"Use comma to separate multiple taxa.")
p.add_option("--rmargin",
default=.3,
type="float",
help="Set blank rmargin to the right [default: %default]")
p.add_option(
"--gffdir",
default=None,
help="The directory that contain GFF files [default: %default]")
p.add_option("--sizes",
default=None,
help="The FASTA file or the sizes file [default: %default]")
opts, args, iopts = set_image_options(p, figsize="8x6")
if len(args) != 1:
sys.exit(not p.print_help())
datafile, = args
outgroup = None
if opts.outgroup:
outgroup = opts.outgroup.split(",")
pf = datafile.rsplit(".", 1)[0]
if tx:
pf = "demo"
else:
tx = open(datafile).read()
logging.debug("Load tree file `{0}`.".format(datafile))
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
draw_tree(root,
tx,
rmargin=opts.rmargin,
outgroup=outgroup,
gffdir=opts.gffdir,
sizes=opts.sizes)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = pf + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def gff(args):
"""
%prog gff *.gff
Draw exons for genes based on gff files. Each gff file should contain only
one gene, and only the "mRNA" and "CDS" feature will be drawn on the canvas.
"""
align_choices = ("left", "center", "right")
p = OptionParser(gff.__doc__)
p.add_option("--align", default="left", choices=align_choices,
help="Horizontal alignment {0} [default: %default]".\
format("|".join(align_choices)))
p.add_option("--noUTR",
default=False,
action="store_true",
help="Do not plot UTRs [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fig = plt.figure(1, (8, 5))
root = fig.add_axes([0, 0, 1, 1])
gffiles = args
ngenes = len(gffiles)
setups, ratio = get_setups(gffiles, canvas=.6, noUTR=opts.noUTR)
align = opts.align
xs = .2 if align == "left" else .8
yinterval = canvas / ngenes
ys = .8
tip = .01
for genename, mrnabed, cdsbeds in setups:
ex = ExonGlyph(root,
xs,
ys,
mrnabed,
cdsbeds,
ratio=ratio,
align=align)
genename = _(genename)
if align == "left":
root.text(xs - tip, ys, genename, ha="right", va="center")
elif align == "right":
root.text(xs + tip, ys, genename, ha="left", va="center")
ys -= yinterval
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = "exons.pdf"
plt.savefig(figname, dpi=300)
logging.debug("Figure saved to `{0}`".format(figname))
def gff(args):
"""
%prog gff *.gff
Draw exons for genes based on gff files. Each gff file should contain only
one gene, and only the "mRNA" and "CDS" feature will be drawn on the canvas.
"""
align_choices = ("left", "center", "right")
p = OptionParser(gff.__doc__)
p.add_option("--align", default="left", choices=align_choices,
help="Horizontal alignment {0} [default: %default]".\
format("|".join(align_choices)))
p.add_option("--noUTR", default=False, action="store_true",
help="Do not plot UTRs [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
fig = plt.figure(1, (8, 5))
root = fig.add_axes([0, 0, 1, 1])
gffiles = args
ngenes = len(gffiles)
setups, ratio = get_setups(gffiles, canvas=.6, noUTR=opts.noUTR)
align = opts.align
xs = .2 if align == "left" else .8
yinterval = canvas / ngenes
ys = .8
tip = .01
for genename, mrnabed, cdsbeds in setups:
ex = ExonGlyph(root, xs, ys, mrnabed, cdsbeds, ratio=ratio, align=align)
genename = _(genename)
if align == "left":
root.text(xs - tip, ys, genename, ha="right", va="center")
elif align == "right":
root.text(xs + tip, ys, genename, ha="left", va="center")
ys -= yinterval
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = "exons.pdf"
plt.savefig(figname, dpi=300)
logging.debug("Figure saved to `{0}`".format(figname))
def main(tx=None):
"""
%prog newicktree
Plot Newick formatted tree. The gene structure can be plotted along if
--gffdir is given. The gff file needs to be `genename.gff`. If --sizes is
on, also show the number of amino acids.
"""
p = OptionParser(main.__doc__)
p.add_option("--outgroup", help="Root the tree using the outgroup. " + \
"Use comma to separate multiple taxa.")
p.add_option("--rmargin", default=.3, type="float",
help="Set blank rmargin to the right [default: %default]")
p.add_option("--gffdir", default=None,
help="The directory that contain GFF files [default: %default]")
p.add_option("--sizes", default=None,
help="The FASTA file or the sizes file [default: %default]")
opts, args, iopts = set_image_options(p, figsize="8x6")
if len(args) != 1:
sys.exit(not p.print_help())
datafile, = args
outgroup = None
if opts.outgroup:
outgroup = opts.outgroup.split(",")
pf = datafile.rsplit(".", 1)[0]
if tx:
pf = "demo"
else:
tx = open(datafile).read()
logging.debug("Load tree file `{0}`.".format(datafile))
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
draw_tree(root, tx, rmargin=opts.rmargin,
outgroup=outgroup, gffdir=opts.gffdir, sizes=opts.sizes)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = pf + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def plot_one_scaffold(scaffoldID, ssizes, sbed, trios, imagename, iopts,
highlights=None):
ntrios = len(trios)
fig = plt.figure(1, (14, 8))
plt.cla()
plt.clf()
root = fig.add_axes([0, 0, 1, 1])
axes = [fig.add_subplot(1, ntrios, x) for x in range(1, ntrios + 1)]
scafsize = ssizes.get_size(scaffoldID)
for trio, ax in zip(trios, axes):
blastf, qsizes, qbed = trio
scaffolding(ax, scaffoldID, blastf, qsizes, ssizes, qbed, sbed,
highlights=highlights)
root.text(.5, .95, _("{0} (size={1})".\
format(scaffoldID, thousands(scafsize))),
size=18, ha="center", color='b')
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
plt.savefig(imagename, dpi=iopts.dpi)
logging.debug("Print image to `{0}` {1}".format(imagename, iopts))
def heatmap(args):
"""
%prog heatmap fastafile chr1
Combine stack plot with heatmap to show abundance of various tracks along
given chromosome. Need to give multiple beds to --stacks and --heatmaps
"""
p = OptionParser(heatmap.__doc__)
p.add_option("--stacks",
default="Exons,Introns,DNA_transposons,Retrotransposons",
help="Features to plot in stackplot [default: %default]")
p.add_option("--heatmaps",
default="Copia,Gypsy,hAT,Helitron,Introns,Exons",
help="Features to plot in heatmaps [default: %default]")
p.add_option("--meres", default=None,
help="Extra centromere / telomere features [default: %default]")
add_window_options(p)
opts, args, iopts = set_image_options(p, args, figsize="8x5")
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, chr = args
window, shift = check_window_options(opts)
stacks = opts.stacks.split(",")
heatmaps = opts.heatmaps.split(",")
stackbeds = [x + ".bed" for x in stacks]
heatmapbeds = [x + ".bed" for x in heatmaps]
stackbins = get_binfiles(stackbeds, fastafile, shift)
heatmapbins = get_binfiles(heatmapbeds, fastafile, shift)
window, shift = check_window_options(opts)
margin = .06
inner = .015
clen = Sizes(fastafile).mapping[chr]
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Gauge
ratio = draw_gauge(root, margin, clen, rightmargin=4 * margin)
yinterval = .3
xx = margin
yy = 1 - margin
yy -= yinterval
xlen = clen / ratio
if "_" in chr:
ca, cb = chr.split("_")
cc = ca[0].upper() + cb
root.add_patch(Rectangle((xx, yy), xlen, yinterval - inner, color=gray))
ax = fig.add_axes([xx, yy, xlen, yinterval - inner])
nbins = clen / shift
if clen % shift:
nbins += 1
owindow = clen / 100
if owindow > window:
window = owindow / shift * shift
stackplot(ax, stackbins, nbins, palette, chr, window, shift)
root.text(xx + inner, yy + yinterval - 2 * inner, cc, va="top")
# Legends
xx += xlen + .01
yspace = (yinterval - inner) / (len(stackbins) + 1)
yy = 1 - margin - yinterval
for s, p in zip(stacks, palette):
s = s.replace("_", " ")
s = Registration.get(s, s)
yy += yspace
root.add_patch(Rectangle((xx, yy), inner, inner, color=p, lw=0))
root.text(xx + 1.5 * inner, yy, s, size=10)
yh = .05 # Heatmap height
# Heatmaps
xx = margin
yy = 1 - margin - yinterval - inner
for s, p in zip(heatmaps, heatmapbins):
s = s.replace("_", " ")
s = Registration.get(s, s)
yy -= yh
m = stackarray(p, chr, window, shift)
Y = np.array([m, m])
root.imshow(Y, extent=(xx, xx + xlen, yy, yy + yh - inner),
interpolation="nearest", aspect="auto")
root.text(xx + xlen + .01, yy, s, size=10)
yy -= yh
meres = opts.meres
if meres:
bed = Bed(meres)
for b in bed:
if b.seqid != chr:
continue
pos = (b.start + b.end) / 2
cpos = pos / ratio
xx = margin + cpos
accn = b.accn.capitalize()
root.add_patch(CirclePolygon((xx, yy), radius=.01, fc="m", ec="m"))
root.text(xx + .014, yy, _(accn), va="center", color="m")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def stack(args):
"""
%prog stack fastafile
Create landscape plots that show the amounts of genic sequences, and repetitive
sequences along the chromosomes.
"""
p = OptionParser(stack.__doc__)
p.add_option("--top", default=10, type="int",
help="Draw the first N chromosomes [default: %default]")
p.add_option("--stacks",
default="Exons,Introns,DNA_transposons,Retrotransposons",
help="Features to plot in stackplot [default: %default]")
p.add_option("--switch",
help="Change chr names based on two-column file [default: %default]")
add_window_options(p)
opts, args, iopts = set_image_options(p, args, figsize="8x8")
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
top = opts.top
window, shift = check_window_options(opts)
switch = opts.switch
if switch:
switch = DictFile(opts.switch)
bedfiles = [x + ".bed" for x in opts.stacks.split(",")]
binfiles = get_binfiles(bedfiles, fastafile, shift)
sizes = Sizes(fastafile)
s = list(sizes.iter_sizes())[:top]
maxl = max(x[1] for x in s)
margin = .08
inner = .02 # y distance between tracks
pf = fastafile.rsplit(".", 1)[0]
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
max_len = s
# Gauge
ratio = draw_gauge(root, margin, maxl)
# Per chromosome
yinterval = (1 - 2 * margin) / (top + 1)
xx = margin
yy = 1 - margin
for chr, clen in s:
yy -= yinterval
xlen = clen / ratio
if "_" in chr:
ca, cb = chr.split("_")
cc = ca[0].upper() + cb
if switch and cc in switch:
cc = "\n".join((cc, "({0})".format(switch[cc])))
root.add_patch(Rectangle((xx, yy), xlen, yinterval - inner, color=gray))
ax = fig.add_axes([xx, yy, xlen, yinterval - inner])
nbins = clen / shift
if clen % shift:
nbins += 1
stackplot(ax, binfiles, nbins, palette, chr, window, shift)
root.text(xx - .04, yy + .5 * (yinterval - inner), cc, ha="center", va="center")
ax.set_xlim(0, nbins)
ax.set_ylim(0, 1)
ax.set_axis_off()
# Legends
yy -= yinterval
xx = margin
for b, p in zip(bedfiles, palette):
b = b.rsplit(".", 1)[0].replace("_", " ")
b = Registration.get(b, b)
root.add_patch(Rectangle((xx, yy), inner, inner, color=p, lw=0))
xx += 2 * inner
root.text(xx, yy, _(b), size=13)
xx += len(b) * .012 + inner
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = pf + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def main():
p = OptionParser(__doc__)
p.add_option("--groups", default=False, action="store_true",
help="The first row contains group info [default: %default]")
p.add_option("--rowgroups", help="Row groupings [default: %default]")
p.add_option("--horizontalbar", default=False, action="store_true",
help="Horizontal color bar [default: vertical]")
p.add_option("--cmap", default="jet",
help="Use this color map [default: %default]")
opts, args, iopts = set_image_options(p, figsize="8x8")
if len(args) != 1:
sys.exit(not p.print_help())
datafile, = args
pf = datafile.rsplit(".", 1)[0]
rowgroups = opts.rowgroups
groups, rows, cols, data = parse_csv(datafile, vmin=1, groups=opts.groups)
cols = [x.replace("ay ", "") for x in cols]
if rowgroups:
fp = open(rowgroups)
rgroups = []
for row in fp:
a, b = row.split()
irows = [rows.index(x) for x in b.split(",")]
rgroups.append((a, min(irows), max(irows)))
plt.rcParams["axes.linewidth"] = 0
xstart = .18
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
ax = fig.add_axes([xstart, .15, .7, .7])
default_cm = cm.get_cmap(opts.cmap)
im = ax.matshow(data, cmap=default_cm, norm=LogNorm(vmin=1, vmax=10000))
nrows, ncols = len(rows), len(cols)
xinterval = .7 / ncols
yinterval = .7 / max(nrows, ncols)
plt.xticks(range(ncols), cols, rotation=45, size=10, ha="center")
plt.yticks(range(nrows), rows, size=10)
for x in ax.get_xticklines() + ax.get_yticklines():
x.set_visible(False)
ax.set_xlim(-.5, ncols - .5)
t = [1, 10, 100, 1000, 10000]
pad = .06
if opts.horizontalbar:
ypos = .5 * (1 - nrows * yinterval) - pad
axcolor = fig.add_axes([.3, ypos, .4, .02])
orientation = "horizontal"
else:
axcolor = fig.add_axes([.9, .3, .02, .4])
orientation = "vertical"
fig.colorbar(im, cax=axcolor, ticks=t, format=_("%d"), orientation=orientation)
if groups:
groups = [(key, len(list(nn))) for key, nn in groupby(groups)]
yy = .5 + .5 * nrows / ncols * .7 + .06
e = .005
sep = -.5
for k, kl in groups:
# Separator in the array area
sep += kl
ax.plot([sep, sep], [-.5, nrows - .5], "w-", lw=2)
# Group labels on the top
kl *= xinterval
root.plot([xstart + e, xstart + kl - e], [yy, yy], "-", color="gray", lw=2)
root.text(xstart + .5 * kl, yy + e, k, ha="center", color="gray")
xstart += kl
if rowgroups:
from jcvi.graphics.glyph import TextCircle
xpos = .04
tip = .015
assert rgroups
ystart = 1 - .5 * (1 - nrows * yinterval)
for gname, start, end in rgroups:
start = ystart - start * yinterval
end = ystart - (end + 1) * yinterval
start -= tip / 3
end += tip / 3
# Bracket the groups
root.plot((xpos, xpos + tip), (start, start), "k-", lw=2)
root.plot((xpos, xpos), (start, end), "k-", lw=2)
root.plot((xpos, xpos + tip), (end, end), "k-", lw=2)
TextCircle(root, xpos, .5 * (start + end), gname)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = pf + "." + opts.cmap + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def histogram(args):
"""
%prog histogram meryl.histogram species K
Plot the histogram based on meryl K-mer distribution, species and N are
only used to annotate the graphic. Find out totalKmers when running
kmer.meryl().
"""
p = OptionParser(histogram.__doc__)
p.add_option("--pdf", default=False, action="store_true",
help="Print PDF instead of ASCII plot [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
histfile, species, N = args
ascii = not opts.pdf
fp = open(histfile)
hist = {}
totalKmers = 0
# Guess the format of the Kmer histogram
soap = False
for row in fp:
if len(row.split()) == 1:
soap = True
break
fp.seek(0)
for rowno, row in enumerate(fp):
if soap:
K = rowno + 1
counts = int(row.strip())
else: # meryl histogram
K, counts = row.split()[:2]
K, counts = int(K), int(counts)
Kcounts = K * counts
totalKmers += Kcounts
hist[K] = counts
history = ["drop"]
for a, b in pairwise(sorted(hist.items())):
Ka, ca = a
Kb, cb = b
if ca <= cb:
status = "rise"
else:
status = "drop"
if history[-1] != status:
history.append(status)
if history == ["drop", "rise", "drop"]:
break
Total_Kmers = int(totalKmers)
Kmer_coverage = Ka
Genome_size = Total_Kmers * 1. / Ka / 1e6
Total_Kmers_msg = "Total {0}-mers: {1}".format(N, Total_Kmers)
Kmer_coverage_msg = "{0}-mer coverage: {1}".format(N, Kmer_coverage)
Genome_size_msg = "Estimated genome size: {0:.1f}Mb".format(Genome_size)
for msg in (Total_Kmers_msg, Kmer_coverage_msg, Genome_size_msg):
print >> sys.stderr, msg
counts = sorted((a, b) for a, b in hist.items() if a <= 100)
x, y = zip(*counts)
title = "{0} genome {1}-mer histogram".format(species, N)
if ascii:
return asciiplot(x, y, title=title)
fig = plt.figure(1, (6, 6))
plt.plot(x, y, 'g-', lw=2, alpha=.5)
ax = plt.gca()
ax.text(.5, .9, _(Total_Kmers_msg),
ha="center", color='b', transform=ax.transAxes)
ax.text(.5, .8, _(Kmer_coverage_msg),
ha="center", color='b', transform=ax.transAxes)
ax.text(.5, .7, _(Genome_size_msg),
ha="center", color='b', transform=ax.transAxes)
ax.set_title(_(title), color='r')
xlabel, ylabel = "Coverage (X)", "Counts"
ax.set_xlabel(_(xlabel), color='r')
ax.set_ylabel(_(ylabel), color='r')
set_human_axis(ax)
imagename = histfile.split(".")[0] + ".pdf"
plt.savefig(imagename, dpi=100)
print >> sys.stderr, "Image saved to `{0}`.".format(imagename)
def heatmap(args):
"""
%prog heatmap fastafile chr1
Combine stack plot with heatmap to show abundance of various tracks along
given chromosome. Need to give multiple beds to --stacks and --heatmaps
"""
p = OptionParser(heatmap.__doc__)
p.add_option("--stacks",
default="Exons,Introns,DNA_transposons,Retrotransposons",
help="Features to plot in stackplot [default: %default]")
p.add_option("--heatmaps",
default="Copia,Gypsy,hAT,Helitron,Introns,Exons",
help="Features to plot in heatmaps [default: %default]")
p.add_option(
"--meres",
default=None,
help="Extra centromere / telomere features [default: %default]")
add_window_options(p)
opts, args, iopts = set_image_options(p, args, figsize="8x5")
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, chr = args
window, shift, subtract = check_window_options(opts)
stacks = opts.stacks.split(",")
heatmaps = opts.heatmaps.split(",")
stackbeds = [x + ".bed" for x in stacks]
heatmapbeds = [x + ".bed" for x in heatmaps]
stackbins = get_binfiles(stackbeds, fastafile, shift, subtract)
heatmapbins = get_binfiles(heatmapbeds, fastafile, shift, subtract)
margin = .06
inner = .015
clen = Sizes(fastafile).mapping[chr]
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Gauge
ratio = draw_gauge(root, margin, clen, rightmargin=4 * margin)
yinterval = .3
xx = margin
yy = 1 - margin
yy -= yinterval
xlen = clen / ratio
if "_" in chr:
ca, cb = chr.split("_")
cc = ca[0].upper() + cb
root.add_patch(Rectangle((xx, yy), xlen, yinterval - inner, color=gray))
ax = fig.add_axes([xx, yy, xlen, yinterval - inner])
nbins = clen / shift
if clen % shift:
nbins += 1
owindow = clen / 100
if owindow > window:
window = owindow / shift * shift
stackplot(ax, stackbins, nbins, palette, chr, window, shift)
root.text(xx + inner, yy + yinterval - 2 * inner, cc, va="top")
# Legends
xx += xlen + .01
yspace = (yinterval - inner) / (len(stackbins) + 1)
yy = 1 - margin - yinterval
for s, p in zip(stacks, palette):
s = s.replace("_", " ")
s = Registration.get(s, s)
yy += yspace
root.add_patch(Rectangle((xx, yy), inner, inner, color=p, lw=0))
root.text(xx + 1.5 * inner, yy, s, size=10)
yh = .05 # Heatmap height
# Heatmaps
xx = margin
yy = 1 - margin - yinterval - inner
for s, p in zip(heatmaps, heatmapbins):
s = s.replace("_", " ")
s = Registration.get(s, s)
yy -= yh
m = stackarray(p, chr, window, shift)
Y = np.array([m, m])
root.imshow(Y,
extent=(xx, xx + xlen, yy, yy + yh - inner),
interpolation="nearest",
aspect="auto")
root.text(xx + xlen + .01, yy, s, size=10)
yy -= yh
meres = opts.meres
if meres:
bed = Bed(meres)
for b in bed:
if b.seqid != chr:
continue
pos = (b.start + b.end) / 2
cpos = pos / ratio
xx = margin + cpos
accn = b.accn.capitalize()
root.add_patch(CirclePolygon((xx, yy), radius=.01, fc="m", ec="m"))
root.text(xx + .014, yy, _(accn), va="center", color="m")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
width = iopts.w
height = iopts.h * ratio
fig = plt.figure(1, (width, height))
root = fig.add_axes([0, 0, 1, 1]) # the whole canvas
ax = fig.add_axes([.1, .1, .8, .8]) # the dot plot
blastplot(ax,
blastfile,
qsizes,
ssizes,
qbed,
sbed,
style=opts.style,
proportional=proportional,
sampleN=opts.sample,
baseticks=True,
stripNames=opts.stripNames)
# add genome names
to_ax_label = lambda fname: _(op.basename(fname).split(".")[0])
gx, gy = [to_ax_label(x.filename) for x in (qsizes, ssizes)]
ax.set_xlabel(gx, size=16)
ax.set_ylabel(gy, size=16)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def coverage(args):
"""
%prog coverage fastafile ctg bedfile1 bedfile2 ..
Plot coverage from a set of BED files that contain the read mappings. The
paired read span will be converted to a new bedfile that contain the happy
mates. ctg is the chr/scf/ctg that you want to plot the histogram on.
If the bedfiles already contain the clone spans, turn on --spans.
"""
from jcvi.formats.bed import mates, bedpe
p = OptionParser(coverage.__doc__)
p.add_option("--ymax", default=None, type="int",
help="Limit ymax [default: %default]")
p.add_option("--spans", default=False, action="store_true",
help="BED files already contain clone spans [default: %default]")
opts, args, iopts = set_image_options(p, args, figsize="8x5")
if len(args) < 3:
sys.exit(not p.print_help())
fastafile, ctg = args[0:2]
bedfiles = args[2:]
sizes = Sizes(fastafile)
size = sizes.mapping[ctg]
fig = plt.figure(1, (iopts.w, iopts.h))
ax = plt.gca()
bins = 100 # smooth the curve
lines = []
legends = []
not_covered = []
yy = .9
for bedfile, c in zip(bedfiles, "rgbcky"):
if not opts.spans:
pf = bedfile.rsplit(".", 1)[0]
matesfile = pf + ".mates"
if need_update(bedfile, matesfile):
matesfile, matesbedfile = mates([bedfile, "--lib"])
bedspanfile = pf + ".spans.bed"
if need_update(matesfile, bedspanfile):
bedpefile, bedspanfile = bedpe([bedfile, "--span",
"--mates={0}".format(matesfile)])
bedfile = bedspanfile
bedsum = Bed(bedfile).sum(seqid=ctg)
notcoveredbases = size - bedsum
legend = _(bedfile.split(".")[0])
msg = "{0}: {1} bp not covered".format(legend, thousands(notcoveredbases))
not_covered.append(msg)
print >> sys.stderr, msg
ax.text(.1, yy, msg, color=c, size=9, transform=ax.transAxes)
yy -= .08
cov = Coverage(bedfile, sizes.filename)
x, y = cov.get_plot_data(ctg, bins=bins)
line, = ax.plot(x, y, '-', color=c, lw=2, alpha=.5)
lines.append(line)
legends.append(legend)
leg = ax.legend(lines, legends, shadow=True, fancybox=True)
leg.get_frame().set_alpha(.5)
ylabel = "Average depth per {0}Kb".format(size / bins / 1000)
ax.set_xlim(0, size)
ax.set_ylim(0, opts.ymax)
ax.set_xlabel(ctg)
ax.set_ylabel(ylabel)
set_human_base_axis(ax)
figname ="{0}.{1}.pdf".format(fastafile, ctg)
plt.savefig(figname, dpi=iopts.dpi)
logging.debug("Figure saved to `{0}` {1}.".format(figname, iopts))
def dotplot(anchorfile, qbed, sbed, image_name, vmin, vmax, iopts,
is_self=False, synteny=False, cmap_text=None):
fp = open(anchorfile)
qorder = qbed.order
sorder = sbed.order
data = []
if cmap_text:
logging.debug("Normalize values to [%.1f, %.1f]" % (vmin, vmax))
for row in fp:
atoms = row.split()
# first two columns are query and subject, and an optional third column
if len(atoms) < 2:
continue
query, subject = atoms[:2]
value = atoms[-1]
try:
value = float(value)
except ValueError:
value = vmax
if value < vmin:
value = vmin
if value > vmax:
value = vmax
if query not in qorder:
#logging.warning("ignore %s" % query)
continue
if subject not in sorder:
#logging.warning("ignore %s" % subject)
continue
qi, q = qorder[query]
si, s = sorder[subject]
nv = vmax - value
data.append((qi, si, nv))
if is_self: # Mirror image
data.append((si, qi, nv))
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1]) # the whole canvas
ax = fig.add_axes([.1, .1, .8, .8]) # the dot plot
sample_number = 5000 # only show random subset
if len(data) > sample_number:
data = sample(data, sample_number)
# the data are plotted in this order, the least value are plotted
# last for aesthetics
data.sort(key=lambda x: -x[2])
default_cm = cm.copper
x, y, c = zip(*data)
ax.scatter(x, y, c=c, s=2, lw=0, cmap=default_cm,
vmin=vmin, vmax=vmax)
if synteny:
clusters = batch_scan(data, qbed, sbed)
draw_box(clusters, ax)
if cmap_text:
draw_cmap(root, cmap_text, vmin, vmax, cmap=default_cm, reverse=True)
xsize, ysize = len(qbed), len(sbed)
logging.debug("xsize=%d ysize=%d" % (xsize, ysize))
xlim = (0, xsize)
ylim = (ysize, 0) # invert the y-axis
xchr_labels, ychr_labels = [], []
ignore = True # tag to mark whether to plot chr name (skip small ones)
ignore_size_x = xsize * .005
ignore_size_y = ysize * .005
# plot the chromosome breaks
for (seqid, beg, end) in qbed.get_breaks():
ignore = abs(end - beg) < ignore_size_x
seqid = seqid.split("_")[-1]
try:
seqid = int(seqid)
seqid = "c%d" % seqid
except:
pass
xchr_labels.append((seqid, (beg + end) / 2, ignore))
ax.plot([beg, beg], ylim, "g-", lw=1)
for (seqid, beg, end) in sbed.get_breaks():
ignore = abs(end - beg) < ignore_size_y
seqid = seqid.split("_")[-1]
try:
seqid = int(seqid)
seqid = "c%d" % seqid
except:
pass
ychr_labels.append((seqid, (beg + end) / 2, ignore))
ax.plot(xlim, [beg, beg], "g-", lw=1)
# plot the chromosome labels
for label, pos, ignore in xchr_labels:
pos = .1 + pos * .8 / xsize
if not ignore:
root.text(pos, .91, label,
ha="center", va="bottom", rotation=45, color="grey")
# remember y labels are inverted
for label, pos, ignore in ychr_labels:
pos = .9 - pos * .8 / ysize
if not ignore:
root.text(.91, pos, label,
va="center", color="grey")
# create a diagonal to separate mirror image for self comparison
if is_self:
ax.plot(xlim, (0, ysize), 'm-', alpha=.5, lw=2)
ax.set_xlim(xlim)
ax.set_ylim(ylim)
# add genome names
to_ax_label = lambda fname: _(op.basename(fname).split(".")[0])
gx, gy = [to_ax_label(x.filename) for x in (qbed, sbed)]
ax.set_xlabel(gx, size=16)
ax.set_ylabel(gy, size=16)
# beautify the numeric axis
for tick in ax.get_xticklines() + ax.get_yticklines():
tick.set_visible(False)
set_human_axis(ax)
plt.setp(ax.get_xticklabels() + ax.get_yticklabels(),
color='gray', size=10)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
def demo(args):
"""
%prog demo
Draw sample gene features to illustrate the various fates of duplicate
genes - to be used in a book chapter.
"""
p = OptionParser(demo.__doc__)
opts, args = p.parse_args(args)
fig = plt.figure(1, (8, 5))
root = fig.add_axes([0, 0, 1, 1])
panel_space = .23
dup_space = .025
# Draw a gene and two regulatory elements at these arbitrary locations
locs = [(.5, .9), # ancestral gene
(.5, .9 - panel_space + dup_space), # identical copies
(.5, .9 - panel_space - dup_space),
(.5, .9 - 2 * panel_space + dup_space), # degenerate copies
(.5, .9 - 2 * panel_space - dup_space),
(.2, .9 - 3 * panel_space + dup_space), # sub-functionalization
(.2, .9 - 3 * panel_space - dup_space),
(.5, .9 - 3 * panel_space + dup_space), # neo-functionalization
(.5, .9 - 3 * panel_space - dup_space),
(.8, .9 - 3 * panel_space + dup_space), # non-functionalization
(.8, .9 - 3 * panel_space - dup_space),
]
default_regulator = "gm"
regulators = [default_regulator,
default_regulator, default_regulator,
"wm", default_regulator,
"wm", "gw",
"wb", default_regulator,
"ww", default_regulator,
]
width = .24
for i, (xx, yy) in enumerate(locs):
regulator = regulators[i]
x1, x2 = xx - .5 * width, xx + .5 * width
Glyph(root, x1, x2, yy)
if i == 9: # upper copy for non-functionalization
continue
# coding region
x1, x2 = xx - .16 * width, xx + .45 * width
Glyph(root, x1, x2, yy, fc="k")
# two regulatory elements
x1, x2 = xx - .4 * width, xx - .28 * width
for xx, fc in zip((x1, x2), regulator):
if fc == 'w':
continue
DoubleCircle(root, xx, yy, fc=fc)
rotation = 30
tip = .02
if i == 0:
ya = yy + tip
root.text(x1, ya, _("Flower"), rotation=rotation, va="bottom")
root.text(x2, ya, _("Root"), rotation=rotation, va="bottom")
elif i == 7:
ya = yy + tip
root.text(x2, ya, _("Leaf"), rotation=rotation, va="bottom")
# Draw arrows between panels (center)
arrow_dist = .08
ar_xpos = .5
for ar_ypos in (.3, .53, .76):
root.annotate(" ", (ar_xpos, ar_ypos),
(ar_xpos, ar_ypos + arrow_dist),
arrowprops=arrowprops)
ar_ypos = .3
for ar_xpos in (.2, .8):
root.annotate(" ", (ar_xpos, ar_ypos),
(.5, ar_ypos + arrow_dist),
arrowprops=arrowprops)
# Duplication, Degeneration
xx = .6
ys = (.76, .53)
processes = ("Duplication", "Degeneration")
for yy, process in zip(ys, processes):
root.text(xx, yy + .02, process, fontweight="bold")
# Label of fates
xs = (.2, .5, .8)
fates = ("Subfunctionalization", "Neofunctionalization",
"Nonfunctionalization")
yy = .05
for xx, fate in zip(xs, fates):
RoundLabel(root, xx, yy, fate)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = "demo.pdf"
plt.savefig(figname, dpi=300)
logging.debug("Figure saved to `{0}`".format(figname))
def stack(args):
"""
%prog stack fastafile
Create landscape plots that show the amounts of genic sequences, and repetitive
sequences along the chromosomes.
"""
p = OptionParser(stack.__doc__)
p.add_option("--top",
default=10,
type="int",
help="Draw the first N chromosomes [default: %default]")
p.add_option("--stacks",
default="Exons,Introns,DNA_transposons,Retrotransposons",
help="Features to plot in stackplot [default: %default]")
p.add_option(
"--switch",
help="Change chr names based on two-column file [default: %default]")
add_window_options(p)
opts, args, iopts = set_image_options(p, args, figsize="8x8")
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
top = opts.top
window, shift, subtract = check_window_options(opts)
switch = opts.switch
if switch:
switch = DictFile(opts.switch)
bedfiles = [x + ".bed" for x in opts.stacks.split(",")]
binfiles = get_binfiles(bedfiles, fastafile, shift, subtract)
sizes = Sizes(fastafile)
s = list(sizes.iter_sizes())[:top]
maxl = max(x[1] for x in s)
margin = .08
inner = .02 # y distance between tracks
pf = fastafile.rsplit(".", 1)[0]
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
max_len = s
# Gauge
ratio = draw_gauge(root, margin, maxl)
# Per chromosome
yinterval = (1 - 2 * margin) / (top + 1)
xx = margin
yy = 1 - margin
for chr, clen in s:
yy -= yinterval
xlen = clen / ratio
if "_" in chr:
ca, cb = chr.split("_")
cc = ca[0].upper() + cb
if switch and cc in switch:
cc = "\n".join((cc, "({0})".format(switch[cc])))
root.add_patch(Rectangle((xx, yy), xlen, yinterval - inner,
color=gray))
ax = fig.add_axes([xx, yy, xlen, yinterval - inner])
nbins = clen / shift
if clen % shift:
nbins += 1
stackplot(ax, binfiles, nbins, palette, chr, window, shift)
root.text(xx - .04,
yy + .5 * (yinterval - inner),
cc,
ha="center",
va="center")
ax.set_xlim(0, nbins)
ax.set_ylim(0, 1)
ax.set_axis_off()
# Legends
yy -= yinterval
xx = margin
for b, p in zip(bedfiles, palette):
b = b.rsplit(".", 1)[0].replace("_", " ")
b = Registration.get(b, b)
root.add_patch(Rectangle((xx, yy), inner, inner, color=p, lw=0))
xx += 2 * inner
root.text(xx, yy, _(b), size=13)
xx += len(b) * .012 + inner
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = pf + "." + iopts.format
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
def qc(args):
"""
%prog qc prefix
Expects data files including:
1. `prefix.bedpe` draws Bezier curve between paired reads
2. `prefix.sizes` draws length of the contig/scaffold
3. `prefix.gaps.bed` mark the position of the gaps in sequence
4. `prefix.bed.coverage` plots the base coverage
5. `prefix.pairs.bed.coverage` plots the clone coverage
See assembly.coverage.posmap() for the generation of these files.
"""
from jcvi.graphics.glyph import Bezier
p = OptionParser(qc.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(p.print_help())
prefix, = args
scf = prefix
# All these files *must* be present in the current folder
bedpefile = prefix + ".bedpe"
fastafile = prefix + ".fasta"
sizesfile = prefix + ".sizes"
gapsbedfile = prefix + ".gaps.bed"
bedfile = prefix + ".bed"
bedpefile = prefix + ".bedpe"
pairsbedfile = prefix + ".pairs.bed"
sizes = Sizes(fastafile).mapping
size = sizes[scf]
fig = plt.figure(1, (8, 5))
root = fig.add_axes([0, 0, 1, 1])
# the scaffold
root.add_patch(Rectangle((.1, .15), .8, .03, fc='k'))
# basecoverage and matecoverage
ax = fig.add_axes([.1, .45, .8, .45])
bins = 200 # Smooth the curve
logging.debug("Coverage curve use window size of {0} bases.".format(window))
basecoverage = Coverage(bedfile, sizesfile)
matecoverage = Coverage(pairsbedfile, sizesfile)
x, y = basecoverage.get_plot_data(scf, bins=bins)
baseline, = ax.plot(x, y, 'g-')
x, y = matecoverage.get_plot_data(scf, bins=bins)
mateline, = ax.plot(x, y, 'r-')
legends = (_("Base coverage"), _("Mate coverage"))
leg = ax.legend((baseline, mateline), legends, shadow=True, fancybox=True)
leg.get_frame().set_alpha(.5)
ax.set_xlim(0, size)
# draw the read pairs
fp = open(bedpefile)
pairs = []
for row in fp:
scf, astart, aend, scf, bstart, bend, clonename = row.split()
astart, bstart = int(astart), int(bstart)
aend, bend = int(aend), int(bend)
start = min(astart, bstart) + 1
end = max(aend, bend)
pairs.append((start, end))
bpratio = .8 / size
cutoff = 1000 # inserts smaller than this are not plotted
# this convert from base => x-coordinate
pos = lambda x: (.1 + x * bpratio)
ypos = .15 + .03
for start, end in pairs:
dist = end - start
if dist < cutoff:
continue
dist = min(dist, 10000)
# 10Kb == .25 canvas height
height = .25 * dist / 10000
xstart = pos(start)
xend = pos(end)
p0 = (xstart, ypos)
p1 = (xstart, ypos + height)
p2 = (xend, ypos + height)
p3 = (xend, ypos)
Bezier(root, p0, p1, p2, p3)
# gaps on the scaffold
fp = open(gapsbedfile)
for row in fp:
b = BedLine(row)
start, end = b.start, b.end
xstart = pos(start)
xend = pos(end)
root.add_patch(Rectangle((xstart, .15), xend - xstart, .03, fc='w'))
root.text(.5, .1, _(scf), color='b', ha="center")
warn_msg = "Only the inserts > {0}bp are shown".format(cutoff)
root.text(.5, .1, _(scf), color='b', ha="center")
root.text(.5, .05, _(warn_msg), color='gray', ha="center")
# clean up and output
set_human_base_axis(ax)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = prefix + ".pdf"
plt.savefig(figname, dpi=300)
logging.debug("Figure saved to `{0}`".format(figname))
image_name = op.splitext(blastfile)[0] + "." + opts.format
plt.rcParams["xtick.major.pad"] = 16
plt.rcParams["ytick.major.pad"] = 16
# Fix the width
xsize, ysize = qsizes.totalsize, ssizes.totalsize
ratio = ysize * 1. / xsize if proportional else 1
width = iopts.w
height = iopts.h * ratio
fig = plt.figure(1, (width, height))
root = fig.add_axes([0, 0, 1, 1]) # the whole canvas
ax = fig.add_axes([.1, .1, .8, .8]) # the dot plot
blastplot(ax, blastfile, qsizes, ssizes, qbed, sbed,
style=opts.style, proportional=proportional, sampleN=opts.sample,
baseticks=True, stripNames=opts.stripNames)
# add genome names
to_ax_label = lambda fname: _(op.basename(fname).split(".")[0])
gx, gy = [to_ax_label(x.filename) for x in (qsizes, ssizes)]
ax.set_xlabel(gx, size=16)
ax.set_ylabel(gy, size=16)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
logging.debug("Print image to `{0}` {1}".format(image_name, iopts))
plt.savefig(image_name, dpi=iopts.dpi)
plt.rcdefaults()
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 demo(args):
"""
%prog demo
Draw sample gene features to illustrate the various fates of duplicate
genes - to be used in a book chapter.
"""
p = OptionParser(demo.__doc__)
opts, args = p.parse_args(args)
fig = plt.figure(1, (8, 5))
root = fig.add_axes([0, 0, 1, 1])
panel_space = .23
dup_space = .025
# Draw a gene and two regulatory elements at these arbitrary locations
locs = [
(.5, .9), # ancestral gene
(.5, .9 - panel_space + dup_space), # identical copies
(.5, .9 - panel_space - dup_space),
(.5, .9 - 2 * panel_space + dup_space), # degenerate copies
(.5, .9 - 2 * panel_space - dup_space),
(.2, .9 - 3 * panel_space + dup_space), # sub-functionalization
(.2, .9 - 3 * panel_space - dup_space),
(.5, .9 - 3 * panel_space + dup_space), # neo-functionalization
(.5, .9 - 3 * panel_space - dup_space),
(.8, .9 - 3 * panel_space + dup_space), # non-functionalization
(.8, .9 - 3 * panel_space - dup_space),
]
default_regulator = "gm"
regulators = [
default_regulator,
default_regulator,
default_regulator,
"wm",
default_regulator,
"wm",
"gw",
"wb",
default_regulator,
"ww",
default_regulator,
]
width = .24
for i, (xx, yy) in enumerate(locs):
regulator = regulators[i]
x1, x2 = xx - .5 * width, xx + .5 * width
Glyph(root, x1, x2, yy)
if i == 9: # upper copy for non-functionalization
continue
# coding region
x1, x2 = xx - .16 * width, xx + .45 * width
Glyph(root, x1, x2, yy, fc="k")
# two regulatory elements
x1, x2 = xx - .4 * width, xx - .28 * width
for xx, fc in zip((x1, x2), regulator):
if fc == 'w':
continue
DoubleCircle(root, xx, yy, fc=fc)
rotation = 30
tip = .02
if i == 0:
ya = yy + tip
root.text(x1, ya, _("Flower"), rotation=rotation, va="bottom")
root.text(x2, ya, _("Root"), rotation=rotation, va="bottom")
elif i == 7:
ya = yy + tip
root.text(x2, ya, _("Leaf"), rotation=rotation, va="bottom")
# Draw arrows between panels (center)
arrow_dist = .08
ar_xpos = .5
for ar_ypos in (.3, .53, .76):
root.annotate(" ", (ar_xpos, ar_ypos), (ar_xpos, ar_ypos + arrow_dist),
arrowprops=arrowprops)
ar_ypos = .3
for ar_xpos in (.2, .8):
root.annotate(" ", (ar_xpos, ar_ypos), (.5, ar_ypos + arrow_dist),
arrowprops=arrowprops)
# Duplication, Degeneration
xx = .6
ys = (.76, .53)
processes = ("Duplication", "Degeneration")
for yy, process in zip(ys, processes):
root.text(xx, yy + .02, process, fontweight="bold")
# Label of fates
xs = (.2, .5, .8)
fates = ("Subfunctionalization", "Neofunctionalization",
"Nonfunctionalization")
yy = .05
for xx, fate in zip(xs, fates):
RoundLabel(root, xx, yy, fate)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = "demo.pdf"
plt.savefig(figname, dpi=300)
logging.debug("Figure saved to `{0}`".format(figname))
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 histogram(args):
"""
%prog histogram meryl.histogram species K
Plot the histogram based on meryl K-mer distribution, species and N are
only used to annotate the graphic. Find out totalKmers when running
kmer.meryl().
"""
p = OptionParser(histogram.__doc__)
p.add_option("--pdf",
default=False,
action="store_true",
help="Print PDF instead of ASCII plot [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
histfile, species, N = args
ascii = not opts.pdf
fp = open(histfile)
hist = {}
totalKmers = 0
# Guess the format of the Kmer histogram
soap = False
for row in fp:
if len(row.split()) == 1:
soap = True
break
fp.seek(0)
for rowno, row in enumerate(fp):
if soap:
K = rowno + 1
counts = int(row.strip())
else: # meryl histogram
K, counts = row.split()[:2]
K, counts = int(K), int(counts)
Kcounts = K * counts
totalKmers += Kcounts
hist[K] = counts
history = ["drop"]
for a, b in pairwise(sorted(hist.items())):
Ka, ca = a
Kb, cb = b
if ca <= cb:
status = "rise"
else:
status = "drop"
if history[-1] != status:
history.append(status)
if history == ["drop", "rise", "drop"]:
break
Total_Kmers = int(totalKmers)
Kmer_coverage = Ka
Genome_size = Total_Kmers * 1. / Ka / 1e6
Total_Kmers_msg = "Total {0}-mers: {1}".format(N, Total_Kmers)
Kmer_coverage_msg = "{0}-mer coverage: {1}".format(N, Kmer_coverage)
Genome_size_msg = "Estimated genome size: {0:.1f}Mb".format(Genome_size)
for msg in (Total_Kmers_msg, Kmer_coverage_msg, Genome_size_msg):
print >> sys.stderr, msg
counts = sorted((a, b) for a, b in hist.items() if a <= 100)
x, y = zip(*counts)
title = "{0} genome {1}-mer histogram".format(species, N)
if ascii:
return asciiplot(x, y, title=title)
fig = plt.figure(1, (6, 6))
plt.plot(x, y, 'g-', lw=2, alpha=.5)
ax = plt.gca()
ax.text(.5,
.9,
_(Total_Kmers_msg),
ha="center",
color='b',
transform=ax.transAxes)
ax.text(.5,
.8,
_(Kmer_coverage_msg),
ha="center",
color='b',
transform=ax.transAxes)
ax.text(.5,
.7,
_(Genome_size_msg),
ha="center",
color='b',
transform=ax.transAxes)
ax.set_title(_(title), color='r')
xlabel, ylabel = "Coverage (X)", "Counts"
ax.set_xlabel(_(xlabel), color='r')
ax.set_ylabel(_(ylabel), color='r')
set_human_axis(ax)
imagename = histfile.split(".")[0] + ".pdf"
plt.savefig(imagename, dpi=100)
print >> sys.stderr, "Image saved to `{0}`.".format(imagename)
