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, 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, 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 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)