def asArtist(self, width, height, margin=20, use_lengths=None,
scale_bar="left", show_params=None, show_internal_labels=False,
label_template=None, edge_label_callback=None, shade_param=None,
max_value=None, font_size=None, **kw):
if use_lengths is None:
use_lengths = self.use_lengths_default
self.updateGeometry(use_lengths=use_lengths)
if width <= 2 * margin:
raise ValueError('%spt not wide enough for %spt margins' %
(width, margin))
if height <= 2 * margin:
raise ValueError('%spt not high enough for %spt margins' %
(height, margin))
width -= 2 * margin
height -= 2 * margin
label_length = len(self.longest_label)
label_width = label_length * 0.8 * (font_size or 10) # not very accurate
(left_labels, right_labels) = self.labelMargins(label_width)
total_label_width = left_labels + right_labels
if width < total_label_width:
raise ValueError('%spt not wide enough for ""%s"' %
(width, self.longest_label))
scale = self.updateCoordinates(width-total_label_width, height)
if shade_param is not None and max_value is None:
for edge in self.postorder(include_self=True):
sp = edge.params.get(shade_param, None)
if max_value is None or sp > max_value:
max_value = sp
renderer = MatplotlibRenderer(shade_param=shade_param,
max_value=max_value, font_size=font_size, **kw)
labelopts = {}
for labelopt in ['show_params', 'show_internal_labels',
'label_template', 'edge_label_callback']:
labelopts[labelopt] = locals()[labelopt]
label_style = DendrogramLabelStyle(**labelopts)
ss = self._draw(renderer, label_style)
if use_lengths:
# Placing the scale properly might take some work,
# for now just always put it in a bottom corner.
unit = 10**min(0.0, numpy.floor(numpy.log10(width/scale/2.0)))
if scale_bar == "right":
x1, x2 = (width-scale*unit, width)
elif scale_bar == "left":
x1, x2 = (-left_labels, scale*unit-left_labels)
else:
assert not scale_bar, scale_bar
if scale_bar:
ss.append(renderer.line(x1, 0.0, x2, 0.0))
ss.append(renderer.string((x1+x2)/2, 5, str(unit), va='bottom', ha='center'))
g = rlg2mpl.Group(*ss)
g.translate(margin+left_labels, margin)
return g
def getShapes(self, span, rotated, height, yrange=None, done_border=False):
if yrange is None:
yrange = self.range
shape_list = []
for track in self.tracks:
if track.needs_border and not done_border:
border = rlg2mpl.Group(
rlg2mpl.Line(span[0],
0,
span[1],
0,
strokeWidth=.5,
strokeColor=colors.black),
rlg2mpl.Line(span[0],
height,
span[1],
height,
strokeWidth=.5,
strokeColor=colors.black))
shape_list.append(border)
done_border = True
shape_list.extend(
track.getShapes(span,
rotated,
height,
yrange=yrange,
done_border=True))
return shape_list
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
trans = TransformScalePart(g.combined_transform)
y = height / 2.0
segments = [[(x1, y), (x2, y)] for (x1, x2) in self.segments]
a = LineCollection(segments, edgecolor='k', facecolor='k')
a.set_linewidth(2)
g.add(a)
a.set_transform(g.combined_transform)
return g
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
posn = 0
for span in self.map.spans:
if not span.lost:
g.add(self._item_shape(
span, self.values[posn:posn+span.length],
height, yrange, rotated))
posn += span.length
return g
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
trans = TransformScalePart(g.combined_transform)
segment = [(.1,0),(.9,0)]
if rotated:
segment = [(y,x) for (x,y) in segment]
a = LineCollection([segment], colors=self.cvalues,
offsets=self.offsets, transOffset=g.combined_transform)
a.set_linewidth(3)
g.add(a)
a.set_transform(trans)
return g
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
(X, Y, I) = (0, 1, 2)
#scaled_axes = [[X, I], [I, Y]][rotated]
scaled_axes = [[X, X], [Y, Y]][rotated]
scaled_axes = [[X, Y], [X, Y]][rotated]
trans = TransformScalePart(g.combined_transform, scaled_axes)
a = CircleCollection([.5], edgecolors=self.cvalues,
facecolors=self.cvalues, offsets=self.offsets,
transOffset=g.combined_transform)
g.add(a)
a.set_transform(trans)
return g
def getShapes(self, span, rotated, height,
yrange=None, done_border=False):
shape_list = [feature.shape(height,
yrange or self.range, rotated) for feature in self.features]
if self.needs_border and not done_border:
border = rlg2mpl.Group(
rlg2mpl.Line(span[0], 0, span[1], 0,
strokeWidth=.5, strokeColor=colors.black),
rlg2mpl.Line(span[0], height, span[1], height,
strokeWidth=.5, strokeColor=colors.black)
)
shape_list = [border] + shape_list
return shape_list
def __call__(self, height, label, map, value, yrange, rotated):
#return self.FeatureClass(label, map)
g = rlg2mpl.Group()
last = first = None
if self.range_required and not yrange:
warnings.warn("'%s' graph values are all zero" % label)
yrange = 1.0
if map.useful and self.one_span:
map = map.getCoveringSpan()
for (i, span) in enumerate(map.spans):
#if last is not None:
# g.add(rlg2mpl.Line(last, height, part.Start, height))
if span.lost or (value is None and self.range_required):
continue
if span.Reverse:
(start, end) = (span.End, span.Start)
(tidy_start, tidy_end) = (span.tidy_end, span.tidy_start)
else:
(start, end) = (span.Start, span.End)
(tidy_start, tidy_end) = (span.tidy_start, span.tidy_end)
shape = self._item_shape(start,
end,
tidy_start,
tidy_end,
height,
value,
yrange,
rotated,
last=i == len(map.spans) - 1)
g.add(shape)
last = end
if first is None:
first = start
if self.showLabel and label and last is not None and height > 7:
font_height = 12 #self.label_font.get_size_in_points()
text_width = llen(label, font_height)
if (text_width < abs(first - last)):
label_shape = Text(
(first + last) / 2,
height / 2,
label,
ha="center",
va="center",
rotation=[0, 90][rotated],
#font_properties=self.label_font,
)
g.add(label_shape)
else:
pass #warnings.warn("couldn't fit feature label '%s'" % label)
return g
def shape(self, height, yrange, rotated):
g = rlg2mpl.Group()
(X, Y, I) = (0, 1, 2)
shapes = [self.shapes, self.rshapes][rotated]
trans = TransformScalePart(g.combined_transform)
artists = []
for (motif, cvalues, offsets) in self.per_shape_values:
shape = shapes[motif]
a = PolyCollection([shape], closed=True,
facecolors=cvalues, edgecolors=cvalues, offsets=offsets,
transOffset=g.combined_transform)
g.add(a)
a.set_transform(trans)
return g
def shape(self, height, yrange, rotated):
rot = 0
if rotated: rot += 90
#if span.Reverse: rot+= 180
g = rlg2mpl.Group()
kw = dict(ha='center', va='baseline', rotation=rot,
font_properties=self.font_properties)
for (motif, cvalues, offsets) in self.per_shape_values:
letter = self.alphabet[motif]
c = len(cvalues)
for (i, (x,y)) in enumerate(offsets):
s = Text(x, y, letter, color=cvalues[i%c], **kw)
g.add(s)
return g
def makeArtist(self, vertical=False):
g = rlg2mpl.Group()
for (y, ym, p) in self._tracks:
smap = self.smap.inverse()
for s in p.getShapes(span=(smap.Start, smap.End),
rotated=vertical,
height=float(p.height),
yrange=self.yrange[p.tag]):
trans = matplotlib.transforms.Affine2D()
trans.translate(0, y)
s.set_transform(s.get_transform() + trans)
g.add(s)
if vertical:
g.rotate(90)
g.scale(-1.0, 1.0)
return g
