def draw_jointplot(figname,
x,
y,
data=None,
kind="reg",
color=None,
xlim=None,
ylim=None,
format="pdf"):
"""
Wraps around sns.jointplot
"""
import seaborn as sns
sns.set_context('talk')
plt.clf()
register = {
"MeanCoverage": "Sample Mean Coverage",
"HD.FDP": "Depth of full spanning reads",
"HD.PDP": "Depth of partial spanning reads",
"HD.PEDP": "Depth of paired-end reads",
"HD.2": "Repeat size of the longer allele"
}
g = sns.jointplot(x,
y,
data=data,
kind=kind,
color=color,
xlim=xlim,
ylim=ylim)
g.ax_joint.set_xlabel(register.get(x, x))
g.ax_joint.set_ylabel(register.get(y, y))
savefig(figname + "." + format, cleanup=False)
def _draw_trees(trees,
nrow=1,
ncol=1,
rmargin=0.3,
iopts=None,
outdir=".",
shfile=None,
**kwargs):
"""
Draw one or multiple trees on one plot.
"""
from jcvi.graphics.tree import draw_tree
if shfile:
SHs = DictFile(shfile, delimiter="\t")
ntrees = len(trees)
n = nrow * ncol
for x in range(int(ceil(float(ntrees) / n))):
fig = plt.figure(1, (iopts.w,
iopts.h)) if iopts else plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
xiv = 1.0 / ncol
yiv = 1.0 / nrow
xstart = list(np.arange(0, 1, xiv)) * nrow
ystart = list(chain(*zip(*[list(np.arange(0, 1, yiv))[::-1]] * ncol)))
for i in range(n * x, n * (x + 1)):
if i == ntrees:
break
ax = fig.add_axes([xstart[i % n], ystart[i % n], xiv, yiv])
f = trees.keys()[i]
tree = trees[f]
try:
SH = SHs[f]
except:
SH = None
draw_tree(ax,
tree,
rmargin=rmargin,
reroot=False,
supportcolor="r",
SH=SH,
**kwargs)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
format = iopts.format if iopts else "pdf"
dpi = iopts.dpi if iopts else 300
if n == 1:
image_name = f.rsplit(".", 1)[0] + "." + format
else:
image_name = "trees{0}.{1}".format(x, format)
image_name = op.join(outdir, image_name)
savefig(image_name, dpi=dpi, iopts=iopts)
plt.clf()
def _draw_trees(trees, nrow=1, ncol=1, rmargin=.3, iopts=None, outdir=".",
shfile=None, **kwargs):
"""
Draw one or multiple trees on one plot.
"""
from jcvi.graphics.tree import draw_tree
if shfile:
SHs = DictFile(shfile, delimiter="\t")
ntrees = len(trees)
n = nrow * ncol
for x in xrange(int(ceil(float(ntrees)/n))):
fig = plt.figure(1, (iopts.w, iopts.h)) if iopts \
else plt.figure(1, (5, 5))
root = fig.add_axes([0, 0, 1, 1])
xiv = 1. / ncol
yiv = 1. / nrow
xstart = list(np.arange(0, 1, xiv)) * nrow
ystart = list(chain(*zip(*[list(np.arange(0, 1, yiv))[::-1]] * ncol)))
for i in xrange(n*x, n*(x+1)):
if i == ntrees:
break
ax = fig.add_axes([xstart[i%n], ystart[i%n], xiv, yiv])
f = trees.keys()[i]
tree = trees[f]
try:
SH = SHs[f]
except:
SH = None
draw_tree(ax, tree, rmargin=rmargin, reroot=False, \
supportcolor="r", SH=SH, **kwargs)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
format = iopts.format if iopts else "pdf"
dpi = iopts.dpi if iopts else 300
if n == 1:
image_name = f.rsplit(".", 1)[0] + "." + format
else:
image_name = "trees{0}.{1}".format(x, format)
image_name = op.join(outdir, image_name)
savefig(image_name, dpi=dpi, iopts=iopts)
plt.clf()
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(
0.5,
0.95,
"{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()
savefig(imagename, dpi=iopts.dpi, iopts=iopts)
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()
savefig(imagename, dpi=iopts.dpi, iopts=iopts)
