def plotFragments(fragment_list,
clip_patch,
color_map,
alignment="vertical",
ax=None):
ax = ax if ax is not None else plt.gca
for fragment in fragment_list:
start = fragment[1]
end = fragment[2]
giemsa_stain = fragment[4]
rect = None
if (alignment == "vertical"):
rect = Rectangle([0, -1 * end],
1,
end - start,
facecolor=color_map[giemsa_stain],
edgecolor="none",
capstyle="butt")
else:
rect = Rectangle([start, 0],
end - start,
1,
facecolor=color_map[giemsa_stain],
edgecolor="none",
capstyle="butt")
rect.set_clip_path(clip_patch)
ax.add_patch(rect)
def _init_legend_box(self, handles, labels):
"""
Initiallize the legend_box. The legend_box is an instance of
the OffsetBox, which is packed with legend handles and
texts. Once packed, their location is calculated during the
drawing time.
"""
fontsize = self._fontsize
text_list = [] # the list of text instances
handle_list = [] # the list of text instances
label_prop = dict(verticalalignment='baseline',
horizontalalignment='left',
fontproperties=self.prop,
)
labelboxes = []
handleboxes = []
height = self._approx_text_height() * 0.7
descent = 0.
for handle, lab in zip(handles, labels):
if isinstance(handle, RegularPolyCollection) or \
isinstance(handle, CircleCollection):
npoints = self.scatterpoints
else:
npoints = self.numpoints
if npoints > 1:
xdata = np.linspace(0.3*fontsize,
(self.handlelength-0.3)*fontsize,
npoints)
xdata_marker = xdata
elif npoints == 1:
xdata = np.linspace(0, self.handlelength*fontsize, 2)
xdata_marker = [0.5*self.handlelength*fontsize]
if isinstance(handle, Line2D):
ydata = ((height-descent)/2.)*np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
legline.update_from(handle)
self._set_artist_props(legline) # after update
legline.set_clip_box(None)
legline.set_clip_path(None)
legline.set_drawstyle('default')
legline.set_marker('None')
handle_list.append(legline)
legline_marker = Line2D(xdata_marker, ydata[:len(xdata_marker)])
legline_marker.update_from(handle)
self._set_artist_props(legline_marker)
legline_marker.set_clip_box(None)
legline_marker.set_clip_path(None)
legline_marker.set_linestyle('None')
legline._legmarker = legline_marker
elif isinstance(handle, Patch):
p = Rectangle(xy=(0., 0.),
width = self.handlelength*fontsize,
height=(height-descent),
)
p.update_from(handle)
self._set_artist_props(p)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
elif isinstance(handle, LineCollection):
ydata = ((height-descent)/2.)*np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
self._set_artist_props(legline)
legline.set_clip_box(None)
legline.set_clip_path(None)
lw = handle.get_linewidth()[0]
dashes = handle.get_dashes()[0]
color = handle.get_colors()[0]
legline.set_color(color)
legline.set_linewidth(lw)
if dashes[0] is not None: # dashed line
legline.set_dashes(dashes[1])
handle_list.append(legline)
elif isinstance(handle, RegularPolyCollection):
ydata = height*self._scatteryoffsets
size_max, size_min = max(handle.get_sizes()),\
min(handle.get_sizes())
if self.scatterpoints < 4:
sizes = [.5*(size_max+size_min), size_max,
size_min]
else:
sizes = (size_max-size_min)*np.linspace(0,1,self.scatterpoints)+size_min
p = type(handle)(handle.get_numsides(),
rotation=handle.get_rotation(),
sizes=sizes,
offsets=zip(xdata_marker,ydata),
transOffset=self.get_transform(),
)
p.update_from(handle)
p.set_figure(self.figure)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
elif isinstance(handle, CircleCollection):
ydata = height*self._scatteryoffsets
size_max, size_min = max(handle.get_sizes()),\
min(handle.get_sizes())
if self.scatterpoints < 4:
sizes = [.5*(size_max+size_min), size_max,
size_min]
else:
sizes = (size_max-size_min)*np.linspace(0,1,self.scatterpoints)+size_min
p = type(handle)(sizes,
offsets=zip(xdata_marker,ydata),
transOffset=self.get_transform(),
)
p.update_from(handle)
p.set_figure(self.figure)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
else:
handle_type = type(handle)
warnings.warn("Legend does not support %s\nUse proxy artist instead.\n\nhttp://matplotlib.sourceforge.net/users/legend_guide.html#using-proxy-artist\n" % (str(handle_type),))
handle_list.append(None)
handle = handle_list[-1]
if handle is not None: # handle is None is the artist is not supproted
textbox = TextArea(lab, textprops=label_prop,
multilinebaseline=True, minimumdescent=True)
text_list.append(textbox._text)
labelboxes.append(textbox)
handlebox = DrawingArea(width=self.handlelength*fontsize,
height=height,
xdescent=0., ydescent=descent)
handlebox.add_artist(handle)
if isinstance(handle, RegularPolyCollection) or \
isinstance(handle, CircleCollection):
handle._transOffset = handlebox.get_transform()
handle.set_transform(None)
if hasattr(handle, "_legmarker"):
handlebox.add_artist(handle._legmarker)
handleboxes.append(handlebox)
if len(handleboxes) > 0:
ncol = min(self._ncol, len(handleboxes))
nrows, num_largecol = divmod(len(handleboxes), ncol)
num_smallcol = ncol-num_largecol
largecol = safezip(range(0, num_largecol*(nrows+1), (nrows+1)),
[nrows+1] * num_largecol)
smallcol = safezip(range(num_largecol*(nrows+1), len(handleboxes), nrows),
[nrows] * num_smallcol)
else:
largecol, smallcol = [], []
handle_label = safezip(handleboxes, labelboxes)
columnbox = []
for i0, di in largecol+smallcol:
itemBoxes = [HPacker(pad=0,
sep=self.handletextpad*fontsize,
children=[h, t], align="baseline")
for h, t in handle_label[i0:i0+di]]
itemBoxes[-1].get_children()[1].set_minimumdescent(False)
columnbox.append(VPacker(pad=0,
sep=self.labelspacing*fontsize,
align="baseline",
children=itemBoxes))
if self._mode == "expand":
mode = "expand"
else:
mode = "fixed"
sep = self.columnspacing*fontsize
self._legend_handle_box = HPacker(pad=0,
sep=sep, align="baseline",
mode=mode,
children=columnbox)
self._legend_title_box = TextArea("")
self._legend_box = VPacker(pad=self.borderpad*fontsize,
sep=self.labelspacing*fontsize,
align="center",
children=[self._legend_title_box,
self._legend_handle_box])
self._legend_box.set_figure(self.figure)
self.texts = text_list
self.legendHandles = handle_list
def _init_legend_box(self, handles, labels):
"""
Initiallize the legend_box. The legend_box is an instance of
the OffsetBox, which is packed with legend handles and
texts. Once packed, their location is calculated during the
drawing time.
"""
fontsize = self.fontsize
# legend_box is a HPacker, horizontally packed with
# columns. Each column is a VPacker, vertically packed with
# legend items. Each legend item is HPacker packed with
# legend handleBox and labelBox. handleBox is an instance of
# offsetbox.DrawingArea which contains legend handle. labelBox
# is an instance of offsetbox.TextArea which contains legend
# text.
text_list = [] # the list of text instances
handle_list = [] # the list of text instances
label_prop = dict(
verticalalignment='baseline',
horizontalalignment='left',
fontproperties=self.prop,
)
labelboxes = []
for l in labels:
textbox = TextArea(l,
textprops=label_prop,
multilinebaseline=True,
minimumdescent=True)
text_list.append(textbox._text)
labelboxes.append(textbox)
handleboxes = []
# The approximate height and descent of text. These values are
# only used for plotting the legend handle.
height = self._approx_text_height() * 0.7
descent = 0.
# each handle needs to be drawn inside a box of (x, y, w, h) =
# (0, -descent, width, height). And their corrdinates should
# be given in the display coordinates.
# NOTE : the coordinates will be updated again in
# _update_legend_box() method.
# The transformation of each handle will be automatically set
# to self.get_trasnform(). If the artist does not uses its
# default trasnform (eg, Collections), you need to
# manually set their transform to the self.get_transform().
for handle in handles:
if isinstance(handle, RegularPolyCollection):
npoints = self.scatterpoints
else:
npoints = self.numpoints
if npoints > 1:
# we put some pad here to compensate the size of the
# marker
xdata = np.linspace(0.3 * fontsize,
(self.handlelength - 0.3) * fontsize,
npoints)
xdata_marker = xdata
elif npoints == 1:
xdata = np.linspace(0, self.handlelength * fontsize, 2)
xdata_marker = [0.5 * self.handlelength * fontsize]
if isinstance(handle, Line2D):
ydata = ((height - descent) / 2.) * np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
legline.update_from(handle)
self._set_artist_props(legline) # after update
legline.set_clip_box(None)
legline.set_clip_path(None)
legline.set_drawstyle('default')
legline.set_marker('None')
handle_list.append(legline)
legline_marker = Line2D(xdata_marker,
ydata[:len(xdata_marker)])
legline_marker.update_from(handle)
self._set_artist_props(legline_marker)
legline_marker.set_clip_box(None)
legline_marker.set_clip_path(None)
legline_marker.set_linestyle('None')
# we don't want to add this to the return list because
# the texts and handles are assumed to be in one-to-one
# correpondence.
legline._legmarker = legline_marker
elif isinstance(handle, Patch):
p = Rectangle(
xy=(0., 0.),
width=self.handlelength * fontsize,
height=(height - descent),
)
p.update_from(handle)
self._set_artist_props(p)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
elif isinstance(handle, LineCollection):
ydata = ((height - descent) / 2.) * np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
self._set_artist_props(legline)
legline.set_clip_box(None)
legline.set_clip_path(None)
lw = handle.get_linewidth()[0]
dashes = handle.get_dashes()[0]
color = handle.get_colors()[0]
legline.set_color(color)
legline.set_linewidth(lw)
legline.set_dashes(dashes)
handle_list.append(legline)
elif isinstance(handle, RegularPolyCollection):
#ydata = self._scatteryoffsets
ydata = height * self._scatteryoffsets
size_max, size_min = max(handle.get_sizes()),\
min(handle.get_sizes())
# we may need to scale these sizes by "markerscale"
# attribute. But other handle types does not seem
# to care about this attribute and it is currently ignored.
if self.scatterpoints < 4:
sizes = [.5 * (size_max + size_min), size_max, size_min]
else:
sizes = (size_max - size_min) * np.linspace(
0, 1, self.scatterpoints) + size_min
p = type(handle)(
handle.get_numsides(),
rotation=handle.get_rotation(),
sizes=sizes,
offsets=zip(xdata_marker, ydata),
transOffset=self.get_transform(),
)
p.update_from(handle)
p.set_figure(self.figure)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
else:
handle_list.append(None)
handlebox = DrawingArea(width=self.handlelength * fontsize,
height=height,
xdescent=0.,
ydescent=descent)
handle = handle_list[-1]
handlebox.add_artist(handle)
if hasattr(handle, "_legmarker"):
handlebox.add_artist(handle._legmarker)
handleboxes.append(handlebox)
# We calculate number of lows in each column. The first
# (num_largecol) columns will have (nrows+1) rows, and remaing
# (num_smallcol) columns will have (nrows) rows.
nrows, num_largecol = divmod(len(handleboxes), self._ncol)
num_smallcol = self._ncol - num_largecol
# starting index of each column and number of rows in it.
largecol = safezip(range(0, num_largecol * (nrows + 1), (nrows + 1)),
[nrows + 1] * num_largecol)
smallcol = safezip(
range(num_largecol * (nrows + 1), len(handleboxes), nrows),
[nrows] * num_smallcol)
handle_label = safezip(handleboxes, labelboxes)
columnbox = []
for i0, di in largecol + smallcol:
# pack handleBox and labelBox into itemBox
itemBoxes = [
HPacker(pad=0,
sep=self.handletextpad * fontsize,
children=[h, t],
align="baseline") for h, t in handle_label[i0:i0 + di]
]
# minimumdescent=False for the text of the last row of the column
itemBoxes[-1].get_children()[1].set_minimumdescent(False)
# pack columnBox
columnbox.append(
VPacker(pad=0,
sep=self.labelspacing * fontsize,
align="baseline",
children=itemBoxes))
if self._mode == "expand":
mode = "expand"
else:
mode = "fixed"
sep = self.columnspacing * fontsize
self._legend_box = HPacker(pad=self.borderpad * fontsize,
sep=sep,
align="baseline",
mode=mode,
children=columnbox)
self._legend_box.set_figure(self.figure)
self.texts = text_list
self.legendHandles = handle_list
def _init_legend_box(self, handles, labels):
"""
Initiallize the legend_box. The legend_box is an instance of
the OffsetBox, which is packed with legend handles and
texts. Once packed, their location is calculated during the
drawing time.
"""
fontsize = self.fontsize
# legend_box is a HPacker, horizontally packed with
# columns. Each column is a VPacker, vertically packed with
# legend items. Each legend item is HPacker packed with
# legend handleBox and labelBox. handleBox is an instance of
# offsetbox.DrawingArea which contains legend handle. labelBox
# is an instance of offsetbox.TextArea which contains legend
# text.
text_list = [] # the list of text instances
handle_list = [] # the list of text instances
label_prop = dict(verticalalignment='baseline',
horizontalalignment='left',
fontproperties=self.prop,
)
labelboxes = []
for l in labels:
textbox = TextArea(l, textprops=label_prop,
multilinebaseline=True, minimumdescent=True)
text_list.append(textbox._text)
labelboxes.append(textbox)
handleboxes = []
# The approximate height and descent of text. These values are
# only used for plotting the legend handle.
height = self._approx_text_height() * 0.7
descent = 0.
# each handle needs to be drawn inside a box of (x, y, w, h) =
# (0, -descent, width, height). And their corrdinates should
# be given in the display coordinates.
# NOTE : the coordinates will be updated again in
# _update_legend_box() method.
# The transformation of each handle will be automatically set
# to self.get_trasnform(). If the artist does not uses its
# default trasnform (eg, Collections), you need to
# manually set their transform to the self.get_transform().
for handle in handles:
if isinstance(handle, RegularPolyCollection):
npoints = self.scatterpoints
else:
npoints = self.numpoints
if npoints > 1:
# we put some pad here to compensate the size of the
# marker
xdata = np.linspace(0.3*fontsize,
(self.handlelength-0.3)*fontsize,
npoints)
xdata_marker = xdata
elif npoints == 1:
xdata = np.linspace(0, self.handlelength*fontsize, 2)
xdata_marker = [0.5*self.handlelength*fontsize]
if isinstance(handle, Line2D):
ydata = ((height-descent)/2.)*np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
legline.update_from(handle)
self._set_artist_props(legline) # after update
legline.set_clip_box(None)
legline.set_clip_path(None)
legline.set_drawstyle('default')
legline.set_marker('None')
handle_list.append(legline)
legline_marker = Line2D(xdata_marker, ydata[:len(xdata_marker)])
legline_marker.update_from(handle)
self._set_artist_props(legline_marker)
legline_marker.set_clip_box(None)
legline_marker.set_clip_path(None)
legline_marker.set_linestyle('None')
# we don't want to add this to the return list because
# the texts and handles are assumed to be in one-to-one
# correpondence.
legline._legmarker = legline_marker
elif isinstance(handle, Patch):
p = Rectangle(xy=(0., 0.),
width = self.handlelength*fontsize,
height=(height-descent),
)
p.update_from(handle)
self._set_artist_props(p)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
elif isinstance(handle, LineCollection):
ydata = ((height-descent)/2.)*np.ones(xdata.shape, float)
legline = Line2D(xdata, ydata)
self._set_artist_props(legline)
legline.set_clip_box(None)
legline.set_clip_path(None)
lw = handle.get_linewidth()[0]
dashes = handle.get_dashes()[0]
color = handle.get_colors()[0]
legline.set_color(color)
legline.set_linewidth(lw)
legline.set_dashes(dashes)
handle_list.append(legline)
elif isinstance(handle, RegularPolyCollection):
#ydata = self._scatteryoffsets
ydata = height*self._scatteryoffsets
size_max, size_min = max(handle.get_sizes()),\
min(handle.get_sizes())
# we may need to scale these sizes by "markerscale"
# attribute. But other handle types does not seem
# to care about this attribute and it is currently ignored.
if self.scatterpoints < 4:
sizes = [.5*(size_max+size_min), size_max,
size_min]
else:
sizes = (size_max-size_min)*np.linspace(0,1,self.scatterpoints)+size_min
p = type(handle)(handle.get_numsides(),
rotation=handle.get_rotation(),
sizes=sizes,
offsets=zip(xdata_marker,ydata),
transOffset=self.get_transform(),
)
p.update_from(handle)
p.set_figure(self.figure)
p.set_clip_box(None)
p.set_clip_path(None)
handle_list.append(p)
else:
handle_list.append(None)
handlebox = DrawingArea(width=self.handlelength*fontsize,
height=height,
xdescent=0., ydescent=descent)
handle = handle_list[-1]
handlebox.add_artist(handle)
if hasattr(handle, "_legmarker"):
handlebox.add_artist(handle._legmarker)
handleboxes.append(handlebox)
# We calculate number of lows in each column. The first
# (num_largecol) columns will have (nrows+1) rows, and remaing
# (num_smallcol) columns will have (nrows) rows.
nrows, num_largecol = divmod(len(handleboxes), self._ncol)
num_smallcol = self._ncol-num_largecol
# starting index of each column and number of rows in it.
largecol = safezip(range(0, num_largecol*(nrows+1), (nrows+1)),
[nrows+1] * num_largecol)
smallcol = safezip(range(num_largecol*(nrows+1), len(handleboxes), nrows),
[nrows] * num_smallcol)
handle_label = safezip(handleboxes, labelboxes)
columnbox = []
for i0, di in largecol+smallcol:
# pack handleBox and labelBox into itemBox
itemBoxes = [HPacker(pad=0,
sep=self.handletextpad*fontsize,
children=[h, t], align="baseline")
for h, t in handle_label[i0:i0+di]]
# minimumdescent=False for the text of the last row of the column
itemBoxes[-1].get_children()[1].set_minimumdescent(False)
# pack columnBox
columnbox.append(VPacker(pad=0,
sep=self.labelspacing*fontsize,
align="baseline",
children=itemBoxes))
if self._mode == "expand":
mode = "expand"
else:
mode = "fixed"
sep = self.columnspacing*fontsize
self._legend_box = HPacker(pad=self.borderpad*fontsize,
sep=sep, align="baseline",
mode=mode,
children=columnbox)
self._legend_box.set_figure(self.figure)
self.texts = text_list
self.legendHandles = handle_list
def plotChromosomeIdeogram(ideogram_bed_filename,
chromosome,
highlighted_region=None,
color_map=giemsa_color_map,
alignment="vertical",
ax=None):
ax = ax if ax is not None else plt.gca()
ideogram_bed_file = open(ideogram_bed_filename, "r")
# load fragments into list
fragment_list_parm = []
fragment_list_qarm = []
for line in ideogram_bed_file:
if (line[0] == "#"):
continue
split_line = line.rstrip().split("\t")
if (not (split_line[0] == chromosome)):
continue
chrom = split_line[0]
start = int(split_line[1])
end = int(split_line[2])
fragment_id = split_line[3]
giemsa_stain = split_line[4]
if (fragment_id[0] == "p"):
fragment_list_parm += [[
chrom, start, end, fragment_id, giemsa_stain
]]
elif (fragment_id[0] == "q"):
fragment_list_qarm += [[
chrom, start, end, fragment_id, giemsa_stain
]]
ideogram_bed_file.close()
p_start = fragment_list_parm[0][1] if not len(
fragment_list_parm) == 0 else None
p_end = fragment_list_parm[-1][2] if not len(
fragment_list_parm) == 0 else None
q_start = fragment_list_qarm[0][1] if not len(
fragment_list_qarm) == 0 else None
q_end = fragment_list_qarm[-1][2] if not len(
fragment_list_qarm) == 0 else None
cap_ext = 2000000
clip_path_patch_parm = None
if (not p_start is None):
# Create Clip path
if (alignment == "vertical"):
vertices = [[0, -1 * cap_ext], [0, -1 * p_end + cap_ext],
[
.5,
bezierMidPoint(-1. * p_end, -1 * p_end + cap_ext,
-1 * p_end + cap_ext, 0.5)
], [1, -1 * p_end + cap_ext], [1, -1. * cap_ext],
[
.5,
bezierMidPoint(0, -1. * cap_ext, -1. * cap_ext, .5)
], [0, -1 * cap_ext]]
else:
vertices = [[1 * cap_ext, 0], [1 * p_end - cap_ext, 0],
[
bezierMidPoint(1. * p_end, 1 * p_end - cap_ext,
1 * p_end - cap_ext, 0.5), .5
], [1 * p_end - cap_ext, 1], [1. * cap_ext, 1],
[
bezierMidPoint(0, 1. * cap_ext, 1. * cap_ext, .5),
.5
], [1 * cap_ext, 0]]
codes = [
Path.MOVETO, Path.LINETO, Path.CURVE3, Path.CURVE3, Path.LINETO,
Path.CURVE3, Path.CURVE3
]
clip_path = Path(vertices, codes=codes)
clip_path_patch_parm = patches.PathPatch(clip_path,
facecolor="none",
linewidth=.5,
capstyle="round")
ax.add_patch(clip_path_patch_parm)
rect = None
if (alignment == "vertical"):
rect = Rectangle((0, -1 * p_end), 1, p_end, facecolor="none")
else:
rect = Rectangle((1 * p_end, 0), p_end, 1, facecolor="none")
rect.set_clip_path(clip_path_patch_parm)
ax.add_patch(rect)
# Plot fragments
plotFragments(fragment_list_parm,
clip_path_patch_parm,
color_map,
alignment=alignment,
ax=ax)
clip_path_path_qarm = None
if (not q_start is None):
if (alignment == "vertical"):
vertices = [[0, -1 * q_start - cap_ext], [0, -1 * q_end + cap_ext],
[
.5,
bezierMidPoint(-1 * q_end, -1 * q_end + cap_ext,
-1 * q_end + cap_ext, .5)
], [1, -1 * q_end + cap_ext],
[1, -1 * q_start - cap_ext],
[
.5,
bezierMidPoint(-1 * q_start,
-1 * q_start - cap_ext,
-1 * q_start - cap_ext, .5)
], [0, -1 * q_start - cap_ext]]
else:
vertices = [[1 * q_start + cap_ext, 0], [1 * q_end - cap_ext, 0],
[
bezierMidPoint(1 * q_end, 1 * q_end - cap_ext,
1 * q_end - cap_ext, .5), .5
], [1 * q_end - cap_ext, 1],
[1 * q_start + cap_ext, 1],
[
bezierMidPoint(1 * q_start, 1 * q_start + cap_ext,
1 * q_start + cap_ext, .5), .5
], [1 * q_start + cap_ext, 0]]
codes = [
Path.MOVETO, Path.LINETO, Path.CURVE3, Path.CURVE3, Path.LINETO,
Path.CURVE3, Path.CURVE3
]
clip_path = Path(vertices, codes=codes)
clip_path_patch_qarm = patches.PathPatch(clip_path,
facecolor="none",
linewidth=.5,
capstyle="round")
ax.add_patch(clip_path_patch_qarm)
rect = None
if (alignment == "vertical"):
rect = Rectangle((1, -1 * q_end),
1, (q_end - q_start),
facecolor="none")
else:
rect = Rectangle((1 * q_end, 1), (q_end - q_start),
1,
facecolor="none")
rect.set_clip_path(clip_path_patch_qarm)
ax.add_patch(rect)
# Plot fragments
plotFragments(fragment_list_qarm,
clip_path_patch_qarm,
color_map,
alignment=alignment,
ax=ax)
ax.axis('off')
if (alignment == "vertical"):
plt.xlim([-.2, 1.2])
plt.ylim([-1 * q_end, 0])
else:
plt.ylim([-.2, 1.2])
plt.xlim([0, 1 * q_end])
if (not highlighted_region is None):
if (alignment == "horizontal"):
rect = Rectangle(
(highlighted_region[1], 0),
width=highlighted_region[2] - highlighted_region[1],
height=1,
capstyle="butt",
linewidth=1,
edgecolor="r",
facecolor="none")
ax.add_patch(rect)
facecolor='w',
zorder=0.5)
# create MNE clipping mask
mne_path = TextPath((0, 0), 'MNE')
dims = mne_path.vertices.max(0) - mne_path.vertices.min(0)
vert = mne_path.vertices - dims / 2.
mult = (plot_dims / dims).min()
mult = [mult, -mult] # y axis is inverted (origin at top left)
offset = plot_dims / 2. - center_fudge
mne_clip = Path(offset + vert * mult, mne_path.codes)
ax.add_patch(PathPatch(mne_clip, color='w', zorder=0, linewidth=0))
# apply clipping mask to field gradient and lines
im.set_clip_path(mne_clip, transform=im.get_transform())
ax.add_patch(rect)
rect.set_clip_path(mne_clip, transform=im.get_transform())
for coll in cs.collections:
coll.set_clip_path(mne_clip, transform=im.get_transform())
# get final position of clipping mask
mne_corners = mne_clip.get_extents().corners()
# add tagline
rcParams.update({'font.sans-serif': ['Cooper Hewitt'], 'font.weight': '300'})
tag_path = TextPath((0, 0), 'MEG + EEG ANALYSIS & VISUALIZATION')
dims = tag_path.vertices.max(0) - tag_path.vertices.min(0)
vert = tag_path.vertices - dims / 2.
mult = tagline_scale_fudge * (plot_dims / dims).min()
mult = [mult, -mult] # y axis is inverted
offset = mne_corners[-1] - np.array(
[mne_clip.get_extents().size[0] / 2., -dims[1]]) - tagline_offset_fudge
tag_clip = Path(offset + vert * mult, tag_path.codes)
