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 get_pts(self, x, y1, y2, width):
w = width / 2
r = width / (3**.5)
pts = []
pts += plot_cap((x, y1 + r), np.radians(range(210, 330)), r)
pts += [[x + w, y1 + r / 2], [x + w, y2 - r / 2]]
pts += plot_cap((x, y2 - r), np.radians(range(30, 150)), r)
pts += [[x - w, y2 - r / 2], [x - w, y1 + r / 2]]
return pts, r
def get_pts(self, x, y1, y2, width):
w = width / 2
r = width / (3 ** .5)
pts = []
pts += plot_cap((x, y1 + r), np.radians(range(210, 330)), r)
pts += [[x + w, y1 + r / 2], [x + w, y2 - r / 2]]
pts += plot_cap((x, y2 - r), np.radians(range(30, 150)), r)
pts += [[x - w, y2 - r / 2], [x - w, y1 + r / 2]]
return pts, r
def __init__(self, ax, x, y1, y2, width=.015, fc="k", fill=False, zorder=2):
"""
Chromosome with positions given in (x, y1) => (x, y2)
"""
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))
def get_pts(self, x1, x2, y, height):
h = height / 2
r = height / (3**.5)
if x2 - x1 < 2 * height: # rectangle for small chromosomes
return [[x1, y + h], [x1, y - h], [x2, y - h], [x2, y + h]], r
pts = []
pts += plot_cap((x1 + r, y), np.radians(range(120, 240)), r)
pts += [[x1 + r / 2, y - h], [x2 - r / 2, y - h]]
pts += plot_cap((x2 - r, y), np.radians(range(-60, 60)), r)
pts += [[x2 - r / 2, y + h], [x1 + r / 2, y + h]]
return pts, r
def get_pts(self, x1, x2, y, height):
h = height / 2
r = height / (3 ** .5)
if x2 - x1 < 2 * height: # rectangle for small chromosomes
return [[x1, y + h], [x1, y - h], [x2, y - h], [x2, y + h]], r
pts = []
pts += plot_cap((x1 + r, y), np.radians(range(120, 240)), r)
pts += [[x1 + r / 2, y - h], [x2 - r / 2, y - h]]
pts += plot_cap((x2 - r, y), np.radians(range(-60, 60)), r)
pts += [[x2 - r / 2, y + h], [x1 + r / 2, y + h]]
return pts, r
def __init__(self, ax, x, y1, y2, y3, width=0.015, fc="k", fill=False, zorder=2):
"""
Chromosome with centromeres at y2 position
"""
pts = []
r = width * 0.5
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 * 0.5, fc="k", ec="k", zorder=zorder))
def amborella(args):
"""
%prog amborella seqids karyotype.layout mcscan.out all.bed synteny.layout
Build a composite figure that calls graphics.karyotype and graphics.synteny.
"""
p = OptionParser(amborella.__doc__)
p.add_option(
"--tree",
help="Display trees on the bottom of the figure [default: %default]")
p.add_option(
"--switch",
help="Rename the seqid with two-column file [default: %default]")
opts, args, iopts = p.set_image_options(args, figsize="8x7")
if len(args) != 5:
sys.exit(not p.print_help())
seqidsfile, klayout, datafile, bedfile, slayout = args
switch = opts.switch
tree = opts.tree
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
Karyotype(fig, root, seqidsfile, klayout)
Synteny(fig, root, datafile, bedfile, slayout, switch=switch, tree=tree)
# legend showing the orientation of the genes
draw_gene_legend(root, .5, .68, .5)
# annotate the WGD events
fc = 'lightslategrey'
x = .05
radius = .012
TextCircle(root, x, .86, '$\gamma$', radius=radius)
TextCircle(root, x, .95, '$\epsilon$', radius=radius)
root.plot([x, x], [.83, .9], ":", color=fc, lw=2)
pts = plot_cap((x, .95), np.radians(range(-70, 250)), .02)
x, y = zip(*pts)
root.plot(x, y, ":", color=fc, lw=2)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
pf = "amborella"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def amborella(args):
"""
%prog amborella seqids karyotype.layout mcscan.out all.bed synteny.layout
Build a composite figure that calls graphics.karyotype and graphics.synteny.
"""
p = OptionParser(amborella.__doc__)
p.add_option("--tree",
help="Display trees on the bottom of the figure [default: %default]")
p.add_option("--switch",
help="Rename the seqid with two-column file [default: %default]")
opts, args, iopts = p.set_image_options(args, figsize="8x7")
if len(args) != 5:
sys.exit(not p.print_help())
seqidsfile, klayout, datafile, bedfile, slayout = args
switch = opts.switch
tree = opts.tree
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
Karyotype(fig, root, seqidsfile, klayout)
Synteny(fig, root, datafile, bedfile, slayout, switch=switch, tree=tree)
# legend showing the orientation of the genes
draw_gene_legend(root, .5, .68, .5)
# annotate the WGD events
fc = 'lightslategrey'
x = .05
radius = .012
TextCircle(root, x, .86, '$\gamma$', radius=radius)
TextCircle(root, x, .95, '$\epsilon$', radius=radius)
root.plot([x, x], [.83, .9], ":", color=fc, lw=2)
pts = plot_cap((x, .95), np.radians(range(-70, 250)), .02)
x, y = zip(*pts)
root.plot(x, y, ":", color=fc, lw=2)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
pf = "amborella"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
