def assign_colors(self, k):
from matplotlib.colors import rgb2hex
colorset = get_map('Paired', 'qualitative', k).mpl_colors
colorset = [rgb2hex(x) for x in colorset]
cs = colorset + ['w'] * (self.n - k - 1)
shuffle(cs)
self.colors = cs[:self.n / 2] + ['k'] + cs[self.n / 2:]
lf, p, rf = self.find_k()
self.exchange(lf, p - 2)
self.exchange(rf, p + 2)
def assign_colors(self, k):
from matplotlib.colors import rgb2hex
colorset = get_map("Paired", "qualitative", k).mpl_colors
colorset = [rgb2hex(x) for x in colorset]
cs = colorset + ["w"] * (self.n - k - 1)
shuffle(cs)
self.colors = cs[:self.n / 2] + ["k"] + cs[self.n / 2:]
lf, p, rf = self.find_k()
self.exchange(lf, p - 2)
self.exchange(rf, p + 2)
def __init__(self, fig, root, canvas, chr, xlim, datadir,
order=None, hlsuffix=None, palette=None, cap=50,
gauge="bottom", plot_label=True, plot_chr_label=True,
gauge_step=5000000, vlines=None, labels_dict={},
diverge=('r', 'g')):
x, y, w, h = canvas
p = .01
root.add_patch(Rectangle((x - p, y - p), w + 2 * p, h + 2 * p, lw=1,
fill=False, ec="darkslategray", zorder=10))
datafiles = glob(op.join(datadir, chr + "*"))
if order:
datafiles = [z for z in datafiles if z.split(".")[1] in order]
datafiles.sort(key=lambda x: order.index(x.split(".")[1]))
ntracks = len(datafiles)
yinterval = h / ntracks
yy = y + h
if palette is None:
# Get the palette
set2 = get_map('Set2', 'qualitative', ntracks).mpl_colors
else:
set2 = [palette] * ntracks
if gauge == "top":
gauge_ax = fig.add_axes([x, yy + p, w, .0001])
adjust_spines(gauge_ax, ["top"])
tpos = yy + .07
elif gauge == "bottom":
gauge_ax = fig.add_axes([x, y - p, w, .0001])
adjust_spines(gauge_ax, ["bottom"])
tpos = y - .07
start, end = xlim
if gauge:
fs = gauge_step < 1000000
setup_gauge_ax(gauge_ax, start, end, gauge_step, float_formatter=fs)
if plot_chr_label:
root.text(x + w / 2, tpos, chr, ha="center", va="center",
color="darkslategray", size=16)
yys = []
for label, datafile, c in zip(order, datafiles, set2):
yy -= yinterval
yys.append(yy)
ax = fig.add_axes([x, yy, w, yinterval * .9])
xy = XYtrack(ax, datafile, color=c)
xy.interpolate(end)
xy.cap(ymax=cap)
if vlines:
xy.vlines(vlines)
if hlsuffix:
hlfile = op.join(datadir, ".".join((label, hlsuffix)))
xy.import_hlfile(hlfile, chr, diverge=diverge)
if plot_label:
label = labels_dict.get(label, label.capitalize())
label = r"\textit{{{0}}}".format(label)
root.text(x - .015, yy + yinterval / 2, label,
ha="right", va="center")
xy.draw()
ax.set_xlim(*xlim)
self.yys = yys
def __init__(self,
fig,
root,
canvas,
chr,
xlim,
datadir,
order=None,
hlsuffix=None,
palette=None,
cap=50,
gauge="bottom",
plot_label=True,
plot_chr_label=True,
gauge_step=5000000,
vlines=None,
labels_dict={},
diverge=('r', 'g')):
x, y, w, h = canvas
p = .01
root.add_patch(
Rectangle((x - p, y - p),
w + 2 * p,
h + 2 * p,
lw=1,
fill=False,
ec="darkslategray",
zorder=10))
datafiles = glob(op.join(datadir, chr + "*"))
if order:
datafiles = [z for z in datafiles if z.split(".")[1] in order]
datafiles.sort(key=lambda x: order.index(x.split(".")[1]))
ntracks = len(datafiles)
yinterval = h / ntracks
yy = y + h
if palette is None:
# Get the palette
set2 = get_map('Set2', 'qualitative', ntracks).mpl_colors
else:
set2 = [palette] * ntracks
if gauge == "top":
gauge_ax = fig.add_axes([x, yy + p, w, .0001])
adjust_spines(gauge_ax, ["top"])
tpos = yy + .07
elif gauge == "bottom":
gauge_ax = fig.add_axes([x, y - p, w, .0001])
adjust_spines(gauge_ax, ["bottom"])
tpos = y - .07
start, end = xlim
if gauge:
fs = gauge_step < 1000000
setup_gauge_ax(gauge_ax,
start,
end,
gauge_step,
float_formatter=fs)
if plot_chr_label:
root.text(x + w / 2,
tpos,
chr,
ha="center",
va="center",
color="darkslategray",
size=16)
yys = []
for label, datafile, c in zip(order, datafiles, set2):
yy -= yinterval
yys.append(yy)
ax = fig.add_axes([x, yy, w, yinterval * .9])
xy = XYtrack(ax, datafile, color=c)
xy.interpolate(end)
xy.cap(ymax=cap)
if vlines:
xy.vlines(vlines)
if hlsuffix:
hlfile = op.join(datadir, ".".join((label, hlsuffix)))
xy.import_hlfile(hlfile, chr, diverge=diverge)
if plot_label:
label = labels_dict.get(label, label.capitalize())
label = r"\textit{{{0}}}".format(label)
root.text(x - .015,
yy + yinterval / 2,
label,
ha="right",
va="center")
xy.draw()
ax.set_xlim(*xlim)
self.yys = yys
