def draw(self, ax, height=.6):
if self.broken is None:
GeneGlyph(ax,
self.x1,
self.x2,
self.y,
height,
tip=2,
color=self.color,
gradient=True)
else:
a, lcolor, rcolor = self.broken
if self.sign < 0:
lcolor, rcolor = rcolor, lcolor
GeneGlyph(ax,
self.x1,
a,
self.y,
height,
tip=0,
color=lcolor,
gradient=True)
GeneGlyph(ax,
a,
self.x2,
self.y,
height,
tip=2,
color=rcolor,
gradient=True)
def plot_diagram(ax, x, y, label="S", title="syntenic", gradient=True):
"""
Part of the diagrams that are re-used. (x, y) marks the center of the
diagram. Label determines the modification to the "S" graph.
"""
trackgap = 0.06
tracklen = 0.12
xa, xb = x - tracklen, x + tracklen
ya, yb = y + trackgap, y - trackgap
hsps = (((60, 150), (50, 130)), ((190, 225), (200, 240)), ((330, 280), (360, 310)))
for yy in (ya, yb):
ax.plot((xa, xb), (yy, yy), "-", color="gray", lw=2, zorder=1)
ytip = 0.015
mrange = 400
m = lambda t: xa + t * 1.0 / mrange * tracklen * 2
for i, ((a, b), (c, d)) in enumerate(hsps):
fb = False
if label == "FB" and i == 1:
c, d = 270, 280
fb = True
if label == "G" and i == 0:
c, d = 120, 65
a, b, c, d = [m(t) for t in (a, b, c, d)]
color = "g" if i == 1 else "r"
GeneGlyph(ax, a, b, ya, 2 * ytip, fc=color, gradient=gradient, zorder=10)
if i == 1 and label in ("F", "G", "FN"):
pass
else:
if fb:
GeneGlyph(
ax, c, d, yb, 2 * ytip, fc="w", tip=0, gradient=gradient, zorder=10
)
else:
GeneGlyph(ax, c, d, yb, 2 * ytip, fc="r", gradient=gradient, zorder=10)
r = Polygon(
((a, ya - ytip), (c, yb + ytip), (d, yb + ytip), (b, ya - ytip)),
fc="r",
alpha=0.2,
)
if i == 1 and label not in ("S", "FB"):
pass
elif i == 0 and label == "G":
pass
else:
ax.add_patch(r)
if label == "FN":
ax.text(x + 0.005, yb, "NNNNN", ha="center", size=7)
title = "{0}: {1}".format(label, title)
ax.text(x, ya + 5 * ytip, title, size=8, ha="center")