def draw_gene_legend(
ax,
x1,
x2,
ytop,
d=0.04,
text=False,
repeat=False,
glyphstyle="box",
):
forward, backward = OrientationPalette.forward, OrientationPalette.backward
ax.plot([x1, x1 + d], [ytop, ytop], ":", color=forward, lw=2)
ax.plot([x1 + d], [ytop], ">", color=forward, mec=forward)
ax.plot([x2, x2 + d], [ytop, ytop], ":", color=backward, lw=2)
ax.plot([x2], [ytop], "<", color=backward, mec="g")
if text:
ax.text(x1 + d / 2, ytop + d / 2, "gene (+)", ha="center")
ax.text(x2 + d / 2, ytop + d / 2, "gene (-)", ha="center")
if repeat:
xr = (x1 + x2 + d) / 2
Glyph(
ax,
xr - d / 2,
xr + d / 2,
ytop,
0.012 * 3 / 4,
gradient=False,
fc="#ff7f00",
style=glyphstyle,
zorder=2,
)
ax.text(xr, ytop + d / 2, "repeat", ha="center")
def draw_gene_legend(ax, x1, x2, ytop, d=.04, text=False, repeat=False):
ax.plot([x1, x1 + d], [ytop, ytop], ":", color=forward, lw=2)
ax.plot([x1 + d], [ytop], ">", color=forward, mec=forward)
ax.plot([x2, x2 + d], [ytop, ytop], ":", color=backward, lw=2)
ax.plot([x2], [ytop], "<", color=backward, mec="g")
if text:
ax.text(x1 + d / 2, ytop + d / 2, "gene (+)", ha="center")
ax.text(x2 + d / 2, ytop + d / 2, "gene (-)", ha="center")
if repeat:
xr = (x1 + x2 + d) / 2
Glyph(ax, xr - d / 2, xr + d / 2, ytop, .012 * 3 / 4, gradient=False,
fc='#ff7f00', zorder=2)
ax.text(xr, ytop + d / 2, "repeat", ha="center")
def __init__(self, ax, ext, layout, bed, scale, switch=None,
chr_label=True, loc_label=True,
pad=.05, vpad=.015, extra_features=None):
x, y = layout.x, layout.y
ratio = layout.ratio
scale /= ratio
self.y = y
lr = layout.rotation
tr = mpl.transforms.Affine2D().\
rotate_deg_around(x, y, lr) + ax.transAxes
inv = ax.transAxes.inverted()
start, end, si, ei, chr, orientation, span = ext
flank = span / scale / 2
xstart, xend = x - flank, x + flank
self.xstart, self.xend = xstart, xend
cv = lambda t: xstart + abs(t - startbp) / scale
hidden = layout.hidden
# Chromosome
if not hidden:
ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
lw=2, zorder=1)
self.genes = genes = bed[si: ei + 1]
startbp, endbp = start.start, end.end
if orientation == '-':
startbp, endbp = endbp, startbp
if switch:
chr = switch.get(chr, chr)
if layout.label:
chr = layout.label
label = "-".join((human_size(startbp, target="Mb", precision=2)[:-2],
human_size(endbp, target="Mb", precision=2)))
height = .012
self.gg = {}
# Genes
for g in genes:
gstart, gend = g.start, g.end
strand = g.strand
if strand == '-':
gstart, gend = gend, gstart
if orientation == '-':
strand = "+" if strand == "-" else "-"
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
self.gg[g.accn] = (a, b)
color = forward if strand == "+" else backward
if not hidden:
gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
gp.set_transform(tr)
# Extra features (like repeats)
if extra_features:
for g in extra_features:
gstart, gend = g.start, g.end
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
gp = Glyph(ax, x1, x2, y, height * 3 / 4, gradient=False,
fc='#ff7f00', zorder=2)
gp.set_transform(tr)
ha, va = layout.ha, layout.va
hpad = .02
if ha == "left":
xx = xstart - hpad
ha = "right"
elif ha == "right":
xx = xend + hpad
ha = "left"
else:
xx = x
ha = "center"
# Tentative solution to labels stick into glyph
magic = 40.
cc = abs(lr) / magic if abs(lr) > magic else 1
if va == "top":
yy = y + cc * pad
elif va == "bottom":
yy = y - cc * pad
else:
yy = y
l = np.array((xx, yy))
trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
l.reshape((1, 2)))[0]
lx, ly = l
if not hidden:
bbox = dict(boxstyle="round", fc='w', ec='w', alpha=.5)
kwargs = dict(ha=ha, va="center",
rotation=trans_angle, bbox=bbox, zorder=10)
# TODO: I spent several hours on trying to make this work - with no
# good solutions. To generate labels on multiple lines, each line
# with a different style is difficult in matplotlib. The only way,
# if you can tolerate an extra dot (.), is to use the recipe below.
#chr_label = r"\noindent " + markup(chr) + r" \\ ." if chr_label else None
#loc_label = r"\noindent . \\ " + label if loc_label else None
chr_label = markup(chr) if chr_label else None
loc_label = label if loc_label else None
if chr_label:
if loc_label:
ax.text(lx, ly + vpad, chr_label, color=layout.color, **kwargs)
ax.text(lx, ly - vpad, loc_label, color="lightslategrey",
size=10, **kwargs)
else:
ax.text(lx, ly, chr_label, color=layout.color, **kwargs)
def __init__(
self,
ax,
ext,
layout,
bed,
scale,
switch=None,
chr_label=True,
loc_label=True,
genelabelsize=0,
pad=0.05,
vpad=0.015,
extra_features=None,
glyphstyle="box",
glyphcolor: BasePalette = OrientationPalette(),
):
x, y = layout.x, layout.y
ratio = layout.ratio
scale /= ratio
self.y = y
lr = layout.rotation
tr = mpl.transforms.Affine2D().rotate_deg_around(x, y, lr) + ax.transAxes
inv = ax.transAxes.inverted()
start, end, si, ei, chr, orientation, span = ext
flank = span / scale / 2
xstart, xend = x - flank, x + flank
self.xstart, self.xend = xstart, xend
cv = lambda t: xstart + abs(t - startbp) / scale
hidden = layout.hidden
# Chromosome
if not hidden:
ax.plot((xstart, xend), (y, y), color="gray", transform=tr, lw=2, zorder=1)
self.genes = genes = bed[si : ei + 1]
startbp, endbp = start.start, end.end
if orientation == "-":
startbp, endbp = endbp, startbp
if switch:
chr = switch.get(chr, chr)
if layout.label:
chr = layout.label
label = "-".join(
(
human_size(startbp, target="Mb", precision=2)[:-2],
human_size(endbp, target="Mb", precision=2),
)
)
height = 0.012
self.gg = {}
# Genes
for g in genes:
gstart, gend = g.start, g.end
strand = g.strand
if strand == "-":
gstart, gend = gend, gstart
if orientation == "-":
strand = "+" if strand == "-" else "-"
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
gene_name = g.accn
self.gg[gene_name] = (a, b)
color, zorder = (
glyphcolor.get_color_and_zorder(strand)
if isinstance(glyphcolor, OrientationPalette)
else glyphcolor.get_color_and_zorder(gene_name)
)
if hidden:
continue
gp = Glyph(
ax,
x1,
x2,
y,
height,
gradient=False,
fc=color,
style=glyphstyle,
zorder=zorder,
)
gp.set_transform(tr)
if genelabelsize:
ax.text(
(x1 + x2) / 2,
y + height / 2 + genelabelsize * vpad / 3,
markup(gene_name),
size=genelabelsize,
rotation=25,
ha="left",
va="center",
color="lightslategray",
)
# Extra features (like repeats)
if extra_features:
for g in extra_features:
gstart, gend = g.start, g.end
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
gp = Glyph(
ax,
x1,
x2,
y,
height * 3 / 4,
gradient=False,
fc="#ff7f00",
style=glyphstyle,
zorder=2,
)
gp.set_transform(tr)
ha, va = layout.ha, layout.va
hpad = 0.02
if ha == "left":
xx = xstart - hpad
ha = "right"
elif ha == "right":
xx = xend + hpad
ha = "left"
else:
xx = x
ha = "center"
# Tentative solution to labels stick into glyph
magic = 40.0
cc = abs(lr) / magic if abs(lr) > magic else 1
if va == "top":
yy = y + cc * pad
elif va == "bottom":
yy = y - cc * pad
else:
yy = y
l = np.array((xx, yy))
trans_angle = ax.transAxes.transform_angles(np.array((lr,)), l.reshape((1, 2)))[
0
]
lx, ly = l
if not hidden:
bbox = dict(boxstyle="round", fc="w", ec="w", alpha=0.5)
kwargs = dict(
ha=ha, va="center", rotation=trans_angle, bbox=bbox, zorder=10
)
# TODO: I spent several hours on trying to make this work - with no
# good solutions. To generate labels on multiple lines, each line
# with a different style is difficult in matplotlib. The only way,
# if you can tolerate an extra dot (.), is to use the recipe below.
# chr_label = r"\noindent " + markup(chr) + r" \\ ." if chr_label else None
# loc_label = r"\noindent . \\ " + label if loc_label else None
chr_label = markup(chr) if chr_label else None
loc_label = label if loc_label else None
if chr_label:
if loc_label:
ax.text(lx, ly + vpad, chr_label, color=layout.color, **kwargs)
ax.text(
lx,
ly - vpad,
loc_label,
color="lightslategrey",
size=10,
**kwargs
)
else:
ax.text(lx, ly, chr_label, color=layout.color, **kwargs)
def __init__(self, ax, ext, layout, bed, scale, switch=None,
chr_label=True, pad=.04, vpad=.012, extra_features=None):
x, y = layout.x, layout.y
ratio = layout.ratio
scale /= ratio
self.y = y
lr = layout.rotation
tr = mpl.transforms.Affine2D().\
rotate_deg_around(x, y, lr) + ax.transAxes
inv = ax.transAxes.inverted()
start, end, si, ei, chr, orientation, span = ext
flank = span / scale / 2
xstart, xend = x - flank, x + flank
self.xstart, self.xend = xstart, xend
cv = lambda t: xstart + abs(t - startbp) / scale
hidden = layout.hidden
# Chromosome
if not hidden:
ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
lw=2, zorder=1)
self.genes = genes = bed[si: ei + 1]
startbp, endbp = start.start, end.end
if orientation == '-':
startbp, endbp = endbp, startbp
if switch:
chr = switch.get(chr, chr)
label = "-".join((human_size(startbp, target="Mb")[:-2],
human_size(endbp, target="Mb")))
height = .012
self.gg = {}
# Genes
for g in genes:
gstart, gend = g.start, g.end
strand = g.strand
if strand == '-':
gstart, gend = gend, gstart
if orientation == '-':
strand = "+" if strand == "-" else "-"
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
self.gg[g.accn] = (a, b)
color = forward if strand == "+" else backward
if not hidden:
gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
gp.set_transform(tr)
# Extra features (like repeats)
if extra_features:
for g in extra_features:
gstart, gend = g.start, g.end
x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
gp = Glyph(ax, x1, x2, y, height * 3 / 4, gradient=False,
fc='#ff7f00', zorder=2)
gp.set_transform(tr)
ha, va = layout.ha, layout.va
hpad = .02
if ha == "left":
xx = xstart - hpad
ha = "right"
elif ha == "right":
xx = xend + hpad
ha = "left"
else:
xx = x
ha = "center"
# Tentative solution to labels stick into glyph
magic = 40.
cc = abs(lr) / magic if abs(lr) > magic else 1
if va == "top":
yy = y + cc * pad
elif va == "bottom":
yy = y - cc * pad - .01
else:
yy = y
l = np.array((xx, yy))
trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
l.reshape((1, 2)))[0]
lx, ly = l
if not hidden and chr_label:
bbox = dict(boxstyle="round", fc='w', ec='w', alpha=.5)
ax.text(lx, ly + vpad, markup(chr), color=layout.color,
ha=ha, va="center", rotation=trans_angle,
bbox=bbox, zorder=10)
ax.text(lx, ly - vpad, label, color="lightslategrey", size=10,
ha=ha, va="center", rotation=trans_angle,
bbox=bbox, zorder=10)
def __init__(self, ax, ext, layout, bed, scale, switch=None, chr_label=True,
pad=.04, vpad=.012):
x, y = layout.x, layout.y
ratio = layout.ratio
scale /= ratio
self.y = y
lr = layout.rotation
tr = Affine2D().rotate_deg_around(x, y, lr) + ax.transAxes
inv = ax.transAxes.inverted()
start, end, si, ei, chr, orientation, span = ext
flank = span / scale / 2
xstart, xend = x - flank, x + flank
self.xstart, self.xend = xstart, xend
cv = lambda t: xstart + abs(t - startbp) / scale
hidden = layout.hidden
# Chromosome
if not hidden:
ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
lw=2, zorder=1)
self.genes = genes = bed[si: ei + 1]
startbp, endbp = start.start, end.end
if orientation == '-':
startbp, endbp = endbp, startbp
if switch:
chr = switch.get(chr, chr)
label = "-".join((human_size(startbp, target="Mb")[:-2],
human_size(endbp, target="Mb")))
height = .012
self.gg = {}
# Genes
for g in genes:
gstart, gend = g.start, g.end
strand = g.strand
if strand == '-':
gstart, gend = gend, gstart
if orientation == '-':
strand = "+" if strand == "-" else "-"
x1, x2 = cv(gstart), cv(gend)
a, b = tr.transform((x1, y)), tr.transform((x2, y))
a, b = inv.transform(a), inv.transform(b)
self.gg[g.accn] = (a, b)
color = "b" if strand == "+" else "g"
if not hidden:
gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
gp.set_transform(tr)
ha, va = layout.ha, layout.va
hpad = .02
if ha == "left":
xx = xstart - hpad
ha = "right"
elif ha == "right":
xx = xend + hpad
ha = "left"
else:
xx = x
ha = "center"
# Tentative solution to labels stick into glyph
magic = 40.
cc = abs(lr) / magic if abs(lr) > magic else 1
if va == "top":
yy = y + cc * pad
elif va == "bottom":
yy = y - cc * pad
else:
yy = y
l = np.array((xx, yy))
trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
l.reshape((1, 2)))[0]
lx, ly = l
if not hidden and chr_label:
ax.text(lx, ly + vpad, markup(chr), color=layout.color,
ha=ha, va="center", rotation=trans_angle)
ax.text(lx, ly - vpad, label, color="k",
ha=ha, va="center", rotation=trans_angle)
def __init__(self,
ax,
ext,
layout,
bed,
scale,
switch=None,
chr_label=True,
pad=.04,
vpad=.012):
x, y = layout.x, layout.y
ratio = layout.ratio
scale /= ratio
self.y = y
lr = layout.rotation
tr = mpl.transforms.Affine2D().\
rotate_deg_around(x, y, lr) + ax.transAxes
inv = ax.transAxes.inverted()
start, end, si, ei, chr, orientation, span = ext
flank = span / scale / 2
xstart, xend = x - flank, x + flank
self.xstart, self.xend = xstart, xend
cv = lambda t: xstart + abs(t - startbp) / scale
hidden = layout.hidden
# Chromosome
if not hidden:
ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
lw=2, zorder=1)
self.genes = genes = bed[si:ei + 1]
startbp, endbp = start.start, end.end
if orientation == '-':
startbp, endbp = endbp, startbp
if switch:
chr = switch.get(chr, chr)
label = "-".join(
(human_size(startbp,
target="Mb")[:-2], human_size(endbp, target="Mb")))
height = .012
self.gg = {}
# Genes
for g in genes:
gstart, gend = g.start, g.end
strand = g.strand
if strand == '-':
gstart, gend = gend, gstart
if orientation == '-':
strand = "+" if strand == "-" else "-"
x1, x2 = cv(gstart), cv(gend)
a, b = tr.transform((x1, y)), tr.transform((x2, y))
a, b = inv.transform(a), inv.transform(b)
self.gg[g.accn] = (a, b)
color = "b" if strand == "+" else "g"
if not hidden:
gp = Glyph(ax,
x1,
x2,
y,
height,
gradient=False,
fc=color,
zorder=3)
gp.set_transform(tr)
ha, va = layout.ha, layout.va
hpad = .02
if ha == "left":
xx = xstart - hpad
ha = "right"
elif ha == "right":
xx = xend + hpad
ha = "left"
else:
xx = x
ha = "center"
# Tentative solution to labels stick into glyph
magic = 40.
cc = abs(lr) / magic if abs(lr) > magic else 1
if va == "top":
yy = y + cc * pad
elif va == "bottom":
yy = y - cc * pad
else:
yy = y
l = np.array((xx, yy))
trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
l.reshape((1, 2)))[0]
lx, ly = l
if not hidden and chr_label:
ax.text(lx,
ly + vpad,
markup(chr),
color=layout.color,
ha=ha,
va="center",
rotation=trans_angle)
ax.text(lx,
ly - vpad,
label,
color="k",
ha=ha,
va="center",
rotation=trans_angle)