def __init__(self,
ax,
x,
y1,
y2,
y3,
width=.015,
fc="k",
fill=False,
zorder=2):
"""
Chromosome with centromeres at y2 position
"""
pts = []
r = width * .5
pts += plot_cap((x, y1 - r), np.radians(range(180)), r)
pts += [[x - r, y1 - r], [x - r, y2 + r]]
pts += plot_cap((x, y2 + r), np.radians(range(180, 360)), r)
pts += [[x + r, y2 + r], [x + r, y1 - r]]
ax.add_patch(Polygon(pts, fc=fc, fill=fill, zorder=zorder))
pts = []
pts += plot_cap((x, y2 - r), np.radians(range(180)), r)
pts += [[x - r, y2 - r], [x - r, y3 + r]]
pts += plot_cap((x, y3 + r), np.radians(range(180, 360)), r)
pts += [[x + r, y3 + r], [x + r, y2 - r]]
ax.add_patch(Polygon(pts, fc=fc, fill=fill, zorder=zorder))
ax.add_patch(
CirclePolygon((x, y2),
radius=r * .5,
fc="k",
ec="k",
zorder=zorder))
def __init__(self,
ax,
x,
y,
label,
radius=.02,
fc="k",
color="w",
size=12,
zorder=4,
**kwargs):
circle = CirclePolygon((x, y), radius, resolution=20, \
fc=fc, ec=fc, zorder=zorder, **kwargs)
ax.add_patch(circle)
ax.text(x,
y,
label,
ha="center",
va="center",
color=color,
size=size,
zorder=zorder + 1,
**kwargs)
def excision(args):
"""
%prog excision
Illustrate the mechanism of illegitimate recombination.
"""
p = OptionParser(__doc__)
opts, args = p.parse_args(args)
fig = plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
plt.plot((0.2, 0.8), (0.6, 0.6), "r-", lw=3)
plt.plot((0.4, 0.6), (0.6, 0.6), "b>-", mfc="g", mec="w", ms=12, lw=3)
plt.plot((0.3, 0.7), (0.5, 0.5), "r-", lw=3)
plt.plot((0.5, ), (0.5, ), "b>-", mfc="g", mec="w", ms=12, lw=3)
# Circle excision
plt.plot((0.5, ), (0.45, ), "b>-", mfc="g", mec="w", ms=12, lw=3)
circle = CirclePolygon((0.5, 0.4), 0.05, fill=False, lw=3, ec="b")
root.add_patch(circle)
arrow_dist = 0.07
ar_xpos, ar_ypos = 0.5, 0.52
root.annotate(" ", (ar_xpos, ar_ypos), (ar_xpos, ar_ypos + arrow_dist),
arrowprops=arrowprops)
RoundLabel(root, 0.2, 0.64, "Gene")
RoundLabel(root, 0.3, 0.54, "Excision")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
figname = fname() + ".pdf"
savefig(figname, dpi=300)
def __init__(self, ax, x, y, radius=.01, **kwargs):
ax.add_patch(
CirclePolygon((x, y), radius * 1.4, resolution=50, fc="w", ec="k"))
ax.add_patch(CirclePolygon((x, y), radius, resolution=50, **kwargs))
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",
)
p.add_option(
"--heatmaps",
default="Copia,Gypsy,hAT,Helitron,Introns,Exons",
help="Features to plot in heatmaps",
)
p.add_option("--meres",
default=None,
help="Extra centromere / telomere features")
add_window_options(p)
opts, args, iopts = p.set_image_options(args, figsize="8x5")
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, chr = args
window, shift, subtract, merge = check_window_options(opts)
stacks = opts.stacks.split(",")
heatmaps = opts.heatmaps.split(",")
stackbeds = get_beds(stacks)
heatmapbeds = get_beds(heatmaps)
stackbins = get_binfiles(stackbeds,
fastafile,
shift,
subtract=subtract,
merge=merge)
heatmapbins = get_binfiles(heatmapbeds,
fastafile,
shift,
subtract=subtract,
merge=merge)
margin = 0.06
inner = 0.015
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 = 0.3
xx = margin
yy = 1 - margin
yy -= yinterval
xlen = clen / ratio
cc = chr
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 = get_nbins(clen, shift)
owindow = clen / 100
if owindow > window:
window = owindow / shift * shift
stackplot(ax, stackbins, nbins, palette, chr, window, shift)
ax.text(
0.1,
0.9,
cc,
va="top",
zorder=100,
transform=ax.transAxes,
bbox=dict(boxstyle="round", fc="w", alpha=0.5),
)
# Legends
xx += xlen + 0.01
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 = 0.05 # 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",
cmap=iopts.cmap,
)
root.text(xx + xlen + 0.01, 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=0.01, fc="m",
ec="m"))
root.text(xx + 0.014, 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
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def __init__(self, ax, x, y, label, radius=.02, fc="k", color="w"):
circle = CirclePolygon((x, y), radius, resolution=20, fc=fc, ec=fc)
ax.add_patch(circle)
ax.text(x, y, label, ha="center", va="center", color=color)