def draw(self, roundrect=False, plot_label=True):
if self.empty:
return
y = self.y
color = self.color
ax = self.ax
xstart = self.xstart
gap = self.gap
va = self.va
nseqids = len(self.seqids)
tr = self.tr
for i, sid in enumerate(self.seqids):
size = self.sizes[sid]
rsize = self.ratio * size
xend = xstart + rsize
hc = HorizontalChromosome(ax,
xstart,
xend,
y,
height=self.height,
lw=self.lw,
fc=color,
roundrect=roundrect)
hc.set_transform(tr)
sid = sid.rsplit("_", 1)[-1]
si = "".join(x for x in sid if x not in string.letters)
si = str(int(si))
xx = (xstart + xend) / 2
xstart = xend + gap
if nseqids > 2 * MaxSeqids and (i + 1) % 10 != 0:
continue
if nseqids < 5:
continue
pad = .02
if va == "bottom":
pad = -pad
TextCircle(ax,
xx,
y + pad,
si,
radius=.01,
fc="w",
color=color,
size=10,
transform=tr)
xp = min(self.xstart / 2, .1) if (self.xstart + self.xend) / 2 <= .5 \
else max(1 - self.end / 2, .92)
label = markup(self.label)
c = color if color != "gainsboro" else "k"
if plot_label:
ax.text(xp,
y + self.height * .6,
label,
ha="center",
color=c,
transform=tr)
def draw(self, roundrect=False, plot_label=True, plot_circles=True,
pad=.03, vpad=.09):
if self.empty:
return
y = self.y
color = self.color
ax = self.ax
xstart = self.xstart
gap = self.gap
va = self.va
nseqids = len(self.seqids)
tr = self.tr
def make_circle_name(sid):
sid = sid.rsplit("_", 1)[-1]
si = "".join(x for x in sid if x in string.digits)
si = str(int(si))
if sid in self.rev:
si += '-'
return si
for i, sid in enumerate(self.seqids):
size = self.sizes[sid]
rsize = self.ratio * size
xend = xstart + rsize
hc = HorizontalChromosome(ax, xstart, xend, y,
height=self.height, lw=self.lw, fc=color,
roundrect=roundrect)
hc.set_transform(tr)
si = make_circle_name(sid)
xx = (xstart + xend) / 2
xstart = xend + gap
step = 2 if nseqids <= 40 else 10
if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
continue
if nseqids < 5:
continue
hpad = -pad if va == "bottom" else pad
if plot_circles:
TextCircle(ax, xx, y + hpad, si, radius=.01,
fc="w", color=color, size=10, transform=tr)
label = markup(self.label)
c = color if color != "gainsboro" else "k"
if plot_label:
if self.label_va == "top":
x, y = self.x, self.y + vpad
elif self.label_va == "bottom":
x, y = self.x, self.y - vpad
else: # "center"
x, y = self.xstart - vpad, self.y
ax.text(x, y, label, ha="center", va="center", color=c, transform=tr)
def draw(self, width=0.03):
HorizontalChromosome(
self.ax,
self.xpad,
1 - self.xpad,
self.ypad - 0.05,
height=width * 1.5,
patch=self.apatch,
lw=2,
)
Chromosome(
self.ax,
self.xpad - 0.05,
self.ypad,
1 - self.ypad,
width=width,
patch=self.bpatch,
patchcolor=self.bpatchcolor,
lw=2,
)
for a, b in zip(self.a, self.b):
self.sax.plot(a, b, "-", color="darkslategrey", lw=2)
self.sax.set_xticklabels([])
self.sax.set_yticklabels([])
self.sax.set_xlim((1, self.amax))
self.sax.set_ylim((1, self.bmax))
normalize_axes(self.ax)
def draw(self, roundrect=False, plot_label=True):
if self.empty:
return
y = self.y
color = self.color
ax = self.ax
xstart = self.xstart
gap = self.gap
va = self.va
nseqids = len(self.seqids)
tr = self.tr
for i, sid in enumerate(self.seqids):
size = self.sizes[sid]
rsize = self.ratio * size
xend = xstart + rsize
hc = HorizontalChromosome(ax, xstart, xend, y,
height=self.height, lw=self.lw, fc=color,
roundrect=roundrect)
hc.set_transform(tr)
sid = sid.rsplit("_", 1)[-1]
si = "".join(x for x in sid if x not in string.letters)
si = str(int(si))
xx = (xstart + xend) / 2
xstart = xend + gap
if nseqids > 2 * MaxSeqids and (i + 1) % 10 != 0:
continue
if nseqids < 5:
continue
pad = .02
if va == "bottom":
pad = - pad
TextCircle(ax, xx, y + pad, si, radius=.01,
fc="w", color=color, size=10, transform=tr)
xp = min(self.xstart / 2, .1) if (self.xstart + self.xend) / 2 <= .5 \
else max(1 - self.xend / 2, .92)
label = markup(self.label)
c = color if color != "gainsboro" else "k"
if plot_label:
ax.text(xp, y + self.height * .6, label,
ha="center", color=c, transform=tr)
def draw(self, width=.03):
HorizontalChromosome(self.ax,
self.xpad,
1 - self.xpad,
self.ypad - width / 2,
height=width * 1.5,
patch=self.apatch,
lw=2)
for r in self.reads:
r.draw(self.sax)
self.sax.set_xlim((1, self.amax))
self.sax.set_ylim((-1, self.ymax))
normalize_axes(self.ax)
self.sax.set_axis_off()
def lms(args):
"""
%prog lms
ALLMAPS cartoon to illustrate LMS metric.
"""
from random import randint
from jcvi.graphics.chromosome import HorizontalChromosome
p = OptionParser(lms.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="6x6", dpi=300)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Panel A
w, h = 0.7, 0.35
ax = fig.add_axes([0.15, 0.6, w, h])
xdata = [x + randint(-3, 3) for x in range(10, 110, 10)]
ydata = [x + randint(-3, 3) for x in range(10, 110, 10)]
ydata[3:7] = ydata[3:7][::-1]
xydata = zip(xdata, ydata)
lis = xydata[:3] + [xydata[4]] + xydata[7:]
lds = xydata[3:7]
xlis, ylis = zip(*lis)
xlds, ylds = zip(*lds)
ax.plot(
xlis,
ylis,
"r-",
lw=12,
alpha=0.3,
solid_capstyle="round",
solid_joinstyle="round",
)
ax.plot(
xlds,
ylds,
"g-",
lw=12,
alpha=0.3,
solid_capstyle="round",
solid_joinstyle="round",
)
ax.plot(xdata, ydata, "k.", mec="k", mfc="w", mew=3, ms=12)
HorizontalChromosome(root, 0.15, 0.15 + w, 0.57, height=0.02, lw=2)
root.text(0.15 + w / 2, 0.55, "Chromosome location (bp)", ha="center", va="top")
ax.text(80, 30, "LIS = 7", color="r", ha="center", va="center")
ax.text(80, 20, "LDS = 4", color="g", ha="center", va="center")
ax.text(80, 10, "LMS = $max$(LIS, LDS) = 7", ha="center", va="center")
normalize_lms_axis(ax, xlim=110, ylim=110)
# Panel B
w = 0.37
p = (0, 45, 75, 110)
ax = fig.add_axes([0.1, 0.12, w, h])
xdata = [x for x in range(10, 110, 10)]
ydata = ydata_orig = [x for x in range(10, 110, 10)]
ydata = ydata[:4] + ydata[7:] + ydata[4:7][::-1]
xydata = zip(xdata, ydata)
lis = xydata[:7]
xlis, ylis = zip(*lis)
ax.plot(
xlis,
ylis,
"r-",
lw=12,
alpha=0.3,
solid_capstyle="round",
solid_joinstyle="round",
)
ax.plot(xdata, ydata, "k.", mec="k", mfc="w", mew=3, ms=12)
ax.vlines(p, 0, 110, colors="beige", lw=3)
normalize_lms_axis(ax, xlim=110, ylim=110)
patch = [0.1 + w * x / 110.0 for x in p]
HorizontalChromosome(root, 0.1, 0.1 + w, 0.09, patch=patch, height=0.02, lw=2)
scaffolds = ("a", "b", "c")
for i, s in enumerate(scaffolds):
xx = (patch[i] + patch[i + 1]) / 2
root.text(xx, 0.09, s, va="center", ha="center")
root.text(0.1 + w / 2, 0.04, "LMS($a||b||c$) = 7", ha="center")
# Panel C
ax = fig.add_axes([0.6, 0.12, w, h])
patch = [0.6 + w * x / 110.0 for x in p]
ydata = ydata_orig
ax.plot(
xdata,
ydata,
"r-",
lw=12,
alpha=0.3,
solid_capstyle="round",
solid_joinstyle="round",
)
ax.plot(xdata, ydata, "k.", mec="k", mfc="w", mew=3, ms=12)
ax.vlines(p, [0], [110], colors="beige", lw=3)
normalize_lms_axis(ax, xlim=110, ylim=110)
HorizontalChromosome(root, 0.6, 0.6 + w, 0.09, patch=patch, height=0.02, lw=2)
scaffolds = ("a", "-c", "b")
for i, s in enumerate(scaffolds):
xx = (patch[i] + patch[i + 1]) / 2
root.text(xx, 0.09, s, va="center", ha="center")
root.text(0.6 + w / 2, 0.04, "LMS($a||-c||b$) = 10", ha="center")
labels = ((0.05, 0.95, "A"), (0.05, 0.48, "B"), (0.55, 0.48, "C"))
panel_labels(root, labels)
normalize_axes(root)
pf = "lms"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def estimategaps(args):
"""
%prog estimategaps JM-4 chr1 JMMale-1
Illustrate ALLMAPS gap estimation algorithm.
"""
p = OptionParser(estimategaps.__doc__)
opts, args, iopts = p.set_image_options(args, figsize="6x6", dpi=300)
if len(args) != 3:
sys.exit(not p.print_help())
pf, seqid, mlg = args
bedfile = pf + ".lifted.bed"
agpfile = pf + ".agp"
function = lambda x: x.cm
cc = Map(bedfile, scaffold_info=True, function=function)
agp = AGP(agpfile)
g = GapEstimator(cc, agp, seqid, mlg, function=function)
pp, chrsize, mlgsize = g.pp, g.chrsize, g.mlgsize
spl, spld = g.spl, g.spld
g.compute_all_gaps(verbose=False)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
# Panel A
xstart, ystart = 0.15, 0.65
w, h = 0.7, 0.3
t = np.linspace(0, chrsize, 1000)
ax = fig.add_axes([xstart, ystart, w, h])
mx, my = zip(*g.scatter_data)
rho = spearmanr(mx, my)
dsg = "g"
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(mx, my, ".", color=set2[3])
ax.plot(t, spl(t), "-", color=dsg)
ax.text(0.05, 0.95, mlg, va="top", transform=ax.transAxes)
normalize_lms_axis(ax, xlim=chrsize, ylim=mlgsize, ylabel="Genetic distance (cM)")
if rho < 0:
ax.invert_yaxis()
# Panel B
ystart -= 0.28
h = 0.25
ax = fig.add_axes([xstart, ystart, w, h])
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(t, spld(t), "-", lw=2, color=dsg)
ax.plot(pp, spld(pp), "o", mfc="w", mec=dsg, ms=5)
normalize_lms_axis(
ax,
xlim=chrsize,
ylim=25 * 1e-6,
xfactor=1e-6,
xlabel="Physical position (Mb)",
yfactor=1000000,
ylabel="Recomb. rate\n(cM / Mb)",
)
ax.xaxis.grid(False)
# Panel C (specific to JMMale-1)
a, b = "scaffold_1076", "scaffold_861"
sizes = dict(
(x.component_id, (x.object_beg, x.object_end, x.component_span, x.orientation))
for x in g.agp
if not x.is_gap
)
a_beg, a_end, asize, ao = sizes[a]
b_beg, b_end, bsize, bo = sizes[b]
gapsize = g.get_gapsize(a)
total_size = asize + gapsize + bsize
ratio = 0.6 / total_size
y = 0.16
pad = 0.03
pb_ratio = w / chrsize
# Zoom
lsg = "lightslategray"
root.plot((0.15 + pb_ratio * a_beg, 0.2), (ystart, ystart - 0.14), ":", color=lsg)
root.plot((0.15 + pb_ratio * b_end, 0.3), (ystart, ystart - 0.08), ":", color=lsg)
ends = []
for tag, size, marker, beg in zip(
(a, b), (asize, bsize), (49213, 81277), (0.2, 0.2 + (asize + gapsize) * ratio)
):
end = beg + size * ratio
marker = beg + marker * ratio
ends.append((beg, end, marker))
root.plot((marker,), (y,), "o", color=lsg)
root.text((beg + end) / 2, y + pad, latex(tag), ha="center", va="center")
HorizontalChromosome(root, beg, end, y, height=0.025, fc="gainsboro")
begs, ends, markers = zip(*ends)
fontprop = dict(color=lsg, ha="center", va="center")
ypos = y + pad * 2
root.plot(markers, (ypos, ypos), "-", lw=2, color=lsg)
root.text(
sum(markers) / 2,
ypos + pad,
"Distance: 1.29cM $\Leftrightarrow$ 211,824bp (6.1 cM/Mb)",
**fontprop
)
ypos = y - pad
xx = markers[0], ends[0]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "34,115bp", **fontprop)
xx = markers[1], begs[1]
root.plot(xx, (ypos, ypos), "-", lw=2, color=lsg)
root.text(sum(xx) / 2, ypos - pad, "81,276bp", **fontprop)
root.plot((ends[0], begs[1]), (y, y), ":", lw=2, color=lsg)
root.text(
sum(markers) / 2,
ypos - 3 * pad,
r"$\textit{Estimated gap size: 96,433bp}$",
color="r",
ha="center",
va="center",
)
labels = ((0.05, 0.95, "A"), (0.05, 0.6, "B"), (0.05, 0.27, "C"))
panel_labels(root, labels)
normalize_axes(root)
pf = "estimategaps"
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def deletion(args):
"""
%prog deletion [deletion-genes|deletion-bases] C2-deletions boleracea.bed
Plot histogram for napus deletions. Can plot deletion-genes or
deletion-bases. The three largest segmental deletions will be highlighted
along with a drawing of the C2 chromosome.
"""
import math
from jcvi.formats.bed import Bed
from jcvi.graphics.chromosome import HorizontalChromosome
from jcvi.graphics.base import kb_formatter
p = OptionParser(deletion.__doc__)
opts, args, iopts = p.set_image_options(args)
if len(args) != 3:
sys.exit(not p.print_help())
deletion_genes, deletions, bed = args
dg = [int(x) for x in open(deletion_genes)]
dsg, lsg = "darkslategray", "lightslategray"
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
ax = fig.add_axes([.1, .1, .8, .8])
minval = 2 if deletion_genes == "deleted-genes" else 2048
bins = np.logspace(math.log(minval, 10), math.log(max(dg), 10), 16)
n, bins, histpatches = ax.hist(dg, bins=bins, \
fc=lsg, alpha=.75)
ax.set_xscale('log', basex=2)
if deletion_genes == "deleted-genes":
ax.xaxis.set_major_formatter(mpl.ticker.FormatStrFormatter('%d'))
ax.set_xlabel('No. of deleted genes in each segment')
else:
ax.xaxis.set_major_formatter(kb_formatter)
ax.set_xlabel('No. of deleted bases in each segment')
ax.yaxis.set_major_formatter(mpl.ticker.FormatStrFormatter('%d'))
ax.set_ylabel('No. of segments')
ax.patch.set_alpha(0.1)
# Draw chromosome C2
na, nb = .45, .85
root.text((na + nb) / 2, .54, "ChrC02", ha="center")
HorizontalChromosome(root, na, nb, .5, height=.025, fc=lsg, fill=True)
order = Bed(bed).order
fp = open(deletions)
scale = lambda x: na + x * (nb - na) / 52886895
for i, row in enumerate(fp):
i += 1
num, genes = row.split()
genes = genes.split("|")
ia, a = order[genes[0]]
ib, b = order[genes[-1]]
mi, mx = a.start, a.end
mi, mx = scale(mi), scale(mx)
root.add_patch(Rectangle((mi, .475), mx - mi, .05, fc="red", ec="red"))
if i == 1: # offset between two adjacent regions for aesthetics
mi -= .015
elif i == 2:
mi += .015
TextCircle(root, mi, .44, str(i), fc="red")
for i, mi in zip(range(1, 4), (.83, .78, .73)):
TextCircle(root, mi, .2, str(i), fc="red")
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = deletion_genes + ".pdf"
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def draw(self, roundrect=False, plot_label=True, pad=.03, vpad=.09):
if self.empty:
return
y = self.y
color = self.color
ax = self.ax
xstart = self.xstart
gap = self.gap
va = self.va
nseqids = len(self.seqids)
tr = self.tr
for i, sid in enumerate(self.seqids):
size = self.sizes[sid]
rsize = self.ratio * size
xend = xstart + rsize
hc = HorizontalChromosome(ax,
xstart,
xend,
y,
height=self.height,
lw=self.lw,
fc=color,
roundrect=roundrect)
hc.set_transform(tr)
sid = sid.rsplit("_", 1)[-1]
si = "".join(x for x in sid if x in string.digits)
si = str(int(si))
xx = (xstart + xend) / 2
xstart = xend + gap
step = 2 if nseqids <= 40 else 10
if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
continue
if nseqids < 5:
continue
hpad = -pad if va == "bottom" else pad
TextCircle(ax,
xx,
y + hpad,
si,
radius=.01,
fc="w",
color=color,
size=10,
transform=tr)
label = markup(self.label)
c = color if color != "gainsboro" else "k"
if plot_label:
if self.label_va == "top":
x, y = self.x, self.y + vpad
va = "bottom"
elif self.label_va == "bottom":
x, y = self.x, self.y - vpad
va = "top"
else: # "center"
x, y = self.xstart - vpad, self.y
va = "center"
ax.text(x,
y,
label,
ha="center",
va="center",
color=c,
transform=tr)
def plot(args):
"""
%prog plot input.bed seqid
Plot the matchings between the reconstructed pseudomolecules and the maps.
Two types of visualizations are available in one canvas:
1. Parallel axes, and matching markers are shown in connecting lines;
2. Scatter plot.
"""
from jcvi.graphics.base import plt, savefig, normalize_axes, \
set2, panel_labels
from jcvi.graphics.chromosome import Chromosome, GeneticMap, \
HorizontalChromosome
p = OptionParser(plot.__doc__)
add_allmaps_plot_options(p)
opts, args, iopts = p.set_image_options(args, figsize="10x6")
if len(args) != 2:
sys.exit(not p.print_help())
inputbed, seqid = args
pf = inputbed.rsplit(".", 1)[0]
bedfile = pf + ".lifted.bed"
agpfile = pf + ".agp"
weightsfile = opts.weightsfile
links = opts.links
function = get_function(opts.distance)
cc = Map(bedfile, function)
allseqids = cc.seqids
mapnames = cc.mapnames
weights = Weights(weightsfile, mapnames)
assert seqid in allseqids, "{0} not in {1}".format(seqid, allseqids)
s = Scaffold(seqid, cc)
mlgs = [k for k, v in s.mlg_counts.items() if v >= links]
mlgsizes = {}
for mlg in mlgs:
mm = cc.extract_mlg(mlg)
mlgsize = max(function(x) for x in mm)
mlgsizes[mlg] = mlgsize
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
ax1 = fig.add_axes([0, 0, .5, 1])
ax2 = fig.add_axes([.5, 0, .5, 1])
# Find the layout first
ystart, ystop = .9, .1
L = Layout(mlgsizes)
coords = L.coords
tip = .02
marker_pos = {}
# Palette
colors = dict((mapname, set2[i]) for i, mapname in enumerate(mapnames))
colors = dict((mlg, colors[mlg.split("-")[0]]) for mlg in mlgs)
rhos = {}
# Parallel coordinates
for mlg, (x, y1, y2) in coords.items():
mm = cc.extract_mlg(mlg)
markers = [(m.accn, function(m)) for m in mm] # exhaustive marker list
xy = [(m.pos, function(m)) for m in mm if m.seqid == seqid]
mx, my = zip(*xy)
rho = spearmanr(mx, my)
rhos[mlg] = rho
flip = rho < 0
g = GeneticMap(ax1, x, y1, y2, markers, tip=tip, flip=flip)
extra = -3 * tip if x < .5 else 3 * tip
ha = "right" if x < .5 else "left"
mapname = mlg.split("-")[0]
tlg = mlg.replace("_", ".") # Latex does not like underscore char
label = "{0} (w={1})".format(tlg, weights[mapname])
ax1.text(x + extra, (y1 + y2) / 2,
label,
color=colors[mlg],
ha=ha,
va="center",
rotation=90)
marker_pos.update(g.marker_pos)
agp = AGP(agpfile)
agp = [x for x in agp if x.object == seqid]
chrsize = max(x.object_end for x in agp)
# Pseudomolecules in the center
r = ystart - ystop
ratio = r / chrsize
f = lambda x: (ystart - ratio * x)
patchstart = [f(x.object_beg) for x in agp if not x.is_gap]
Chromosome(ax1, .5, ystart, ystop, width=2 * tip, patch=patchstart, lw=2)
label = "{0} ({1})".format(seqid, human_size(chrsize, precision=0))
ax1.text(.5, ystart + tip, label, ha="center")
scatter_data = defaultdict(list)
# Connecting lines
for b in s.markers:
marker_name = b.accn
if marker_name not in marker_pos:
continue
cx = .5
cy = f(b.pos)
mx = coords[b.mlg][0]
my = marker_pos[marker_name]
extra = -tip if mx < cx else tip
extra *= 1.25 # leave boundaries for aesthetic reasons
cx += extra
mx -= extra
ax1.plot((cx, mx), (cy, my), "-", color=colors[b.mlg])
scatter_data[b.mlg].append((b.pos, function(b)))
# Scatter plot, same data as parallel coordinates
xstart, xstop = sorted((ystart, ystop))
f = lambda x: (xstart + ratio * x)
pp = [x.object_beg for x in agp if not x.is_gap]
patchstart = [f(x) for x in pp]
HorizontalChromosome(ax2,
xstart,
xstop,
ystop,
height=2 * tip,
patch=patchstart,
lw=2)
gap = .03
ratio = (r - gap * len(mlgs) - tip) / sum(mlgsizes.values())
tlgs = []
for mlg, mlgsize in sorted(mlgsizes.items()):
height = ratio * mlgsize
ystart -= height
xx = .5 + xstart / 2
width = r / 2
color = colors[mlg]
ax = fig.add_axes([xx, ystart, width, height])
ypos = ystart + height / 2
ystart -= gap
sd = scatter_data[mlg]
xx, yy = zip(*sd)
ax.vlines(pp, 0, mlgsize, colors="beige")
ax.plot(xx, yy, ".", color=color)
rho = rhos[mlg]
ax.text(.5,
1 - .4 * gap / height,
r"$\rho$={0:.3f}".format(rho),
ha="center",
va="top",
transform=ax.transAxes,
color="gray")
tlg = mlg.replace("_", ".")
tlgs.append((tlg, ypos, color))
ax.set_xlim(0, chrsize)
ax.set_ylim(0, mlgsize)
ax.set_xticks([])
while height / len(ax.get_yticks()) < .03 and len(
ax.get_yticks()) >= 2:
ax.set_yticks(ax.get_yticks()[::2]) # Sparsify the ticks
yticklabels = [int(x) for x in ax.get_yticks()]
ax.set_yticklabels(yticklabels, family='Helvetica')
if rho < 0:
ax.invert_yaxis()
for i, (tlg, ypos, color) in enumerate(tlgs):
ha = "center"
if len(tlgs) > 4:
ha = "right" if i % 2 else "left"
root.text(.5, ypos, tlg, color=color, rotation=90, ha=ha, va="center")
if opts.panels:
labels = ((.04, .96, 'A'), (.48, .96, 'B'))
panel_labels(root, labels)
normalize_axes((ax1, ax2, root))
image_name = seqid + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
plt.close(fig)
def composite(args):
"""
%prog composite fastafile chr1
Combine line plots, feature bars and alt-bars, different data types
specified in options. Inputs must be BED-formatted. Three types of viz are
currently supported:
--lines: traditional line plots, useful for plotting feature freq
--bars: show where the extent of features are
--altbars: similar to bars, yet in two alternating tracks, e.g. scaffolds
"""
from jcvi.graphics.chromosome import HorizontalChromosome
p = OptionParser(composite.__doc__)
p.add_option("--lines", help="Features to plot in lineplot")
p.add_option("--bars", help="Features to plot in bars")
p.add_option("--altbars", help="Features to plot in alt-bars")
p.add_option(
"--fatten",
default=False,
action="store_true",
help="Help visualize certain narrow features",
)
p.add_option(
"--mode",
default="span",
choices=("span", "count", "score"),
help="Accumulate feature based on",
)
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)
linebeds, barbeds, altbarbeds = [], [], []
fatten = opts.fatten
if opts.lines:
lines = opts.lines.split(",")
linebeds = get_beds(lines)
if opts.bars:
bars = opts.bars.split(",")
barbeds = get_beds(bars)
if opts.altbars:
altbars = opts.altbars.split(",")
altbarbeds = get_beds(altbars)
linebins = get_binfiles(linebeds,
fastafile,
shift,
mode=opts.mode,
merge=merge)
margin = 0.12
clen = Sizes(fastafile).mapping[chr]
nbins = get_nbins(clen, shift)
plt.rcParams["xtick.major.size"] = 0
plt.rcParams["ytick.major.size"] = 0
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
root.text(0.5, 0.95, chr, ha="center", color="darkslategray")
xstart, xend = margin, 1 - margin
xlen = xend - xstart
ratio = xlen / clen
# Line plots
ax = fig.add_axes([xstart, 0.6, xlen, 0.3])
lineplot(ax, linebins, nbins, chr, window, shift)
# Bar plots
yy = 0.5
yinterval = 0.08
xs = lambda x: xstart + ratio * x
r = 0.01
fattend = 0.0025
for bb in barbeds:
root.text(xend + 0.01, yy, bb.split(".")[0], va="center")
HorizontalChromosome(root, xstart, xend, yy, height=0.02)
bb = Bed(bb)
for b in bb:
start, end = xs(b.start), xs(b.end)
span = end - start
if fatten and span < fattend:
span = fattend
root.add_patch(
Rectangle((start, yy - r),
span,
2 * r,
lw=0,
fc="darkslategray"))
yy -= yinterval
# Alternative bar plots
offset = r / 2
for bb in altbarbeds:
root.text(xend + 0.01, yy, bb.split(".")[0], va="center")
bb = Bed(bb)
for i, b in enumerate(bb):
start, end = xs(b.start), xs(b.end)
span = end - start
if span < 0.0001:
continue
offset = -offset
root.add_patch(
Rectangle((start, yy + offset),
end - start,
0.003,
lw=0,
fc="darkslategray"))
yy -= yinterval
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 draw(self,
roundrect=False,
plot_label=True,
plot_circles=True,
pad=0.03,
vpad=0.09):
if self.empty:
return
y = self.y
color = self.color
ax = self.ax
xstart = self.xstart
gap = self.gap
va = self.va
nseqids = len(self.seqids)
tr = self.tr
for i, sid in enumerate(self.seqids):
size = self.sizes[sid]
rsize = self.ratio * size
xend = xstart + rsize
hc = HorizontalChromosome(
ax,
xstart,
xend,
y,
height=self.height,
lw=self.lw,
fc=color,
roundrect=roundrect,
)
hc.set_transform(tr)
si = make_circle_name(sid, self.rev)
xx = (xstart + xend) / 2
xstart = xend + gap
step = 2 if nseqids <= 40 else 10
if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
continue
if nseqids < 5:
continue
hpad = -pad if va == "bottom" else pad
if plot_circles:
TextCircle(
ax,
xx,
y + hpad,
si,
fc="w",
color=color,
size=10,
transform=tr,
)
label = markup(self.label)
c = color if color != "gainsboro" else "k"
if plot_label:
if self.label_va == "top":
x, y = self.x, self.y + vpad
elif self.label_va == "bottom":
x, y = self.x, self.y - vpad
else: # "center"
x, y = self.xstart - vpad / 2, self.y
ax.text(x,
y,
label,
ha="center",
va="center",
color=c,
transform=tr)