def __init__(self, start_ls, end_ls, y=0, width=0.001, x_offset=0, is_arrow=True, length_includes_head=True, \
head_width=None, head_length=None, shape='full', overhang=0, \
head_starts_at_zero=False,**kwargs):
if head_width is None:
head_width = 2 * width
if head_length is None:
head_length = 1 / (2.0 * abs(end_ls[0] - start_ls[0]))
distance = abs(end_ls[-1] - start_ls[0])
if length_includes_head:
length = distance
else:
length = distance + head_length
no_of_blocks = len(start_ls)
if not distance:
verts_ls = [] #display nothing if empty
else:
"""
start by drawing horizontal arrow, point (tip of the arrow) at (0,0). the whole arrow sticks on the x-axis (<=0 part)
Notice: the XY -coordination is not the usual math coordination system. it's canvas coordination. (0,0) is top left. horizontal is y-axis. vertical is x-axis.
start from the last block, reversely to the 1st block
"""
verts_ls = []
for i in range(no_of_blocks):
block_start = start_ls[i]
block_end = end_ls[i]
verts = [[block_start, width / 2.0 + y],
[block_start, -width / 2.0 + y],
[block_end, -width / 2.0 + y],
[block_end, width / 2.0 + y]]
verts_ls.append(verts)
PolyCollection.__init__(self, verts_ls, **kwargs)
def __init__(self, ax, *args, **kw):
self.ax = ax
X, Y, U, V, C = self._parse_args(*args)
self.X = X
self.Y = Y
self.N = len(X)
self.scale = kw.pop('scale', None)
self.headwidth = kw.pop('headwidth', 3)
self.headlength = float(kw.pop('headlength', 5))
self.headaxislength = kw.pop('headaxislength', 4.5)
self.minshaft = kw.pop('minshaft', 1)
self.minlength = kw.pop('minlength', 1)
self.units = kw.pop('units', 'width')
self.width = kw.pop('width', None)
self.color = kw.pop('color', 'k')
self.pivot = kw.pop('pivot', 'tail')
kw.setdefault('facecolors', self.color)
kw.setdefault('linewidths', (0,))
PolyCollection.__init__(self, None, offsets=zip(X, Y),
transOffset=ax.transData, **kw)
self.polykw = kw
self.set_UVC(U, V, C)
self._initialized = False
self.keyvec = None
self.keytext = None
def __init__(self, start_ls, end_ls, y=0, width=0.001, x_offset=0, is_arrow=True, length_includes_head=True, \ head_width=None, head_length=None, shape='full', overhang=0, \ head_starts_at_zero=False,**kwargs): if head_width is None: head_width = 2 * width if head_length is None: head_length = 1/(2.0 * abs(end_ls[0]-start_ls[0])) distance = abs(end_ls[-1]-start_ls[0]) if length_includes_head: length=distance else: length=distance+head_length no_of_blocks = len(start_ls) if not distance: verts_ls = [] #display nothing if empty else: """ start by drawing horizontal arrow, point (tip of the arrow) at (0,0). the whole arrow sticks on the x-axis (<=0 part) Notice: the XY -coordination is not the usual math coordination system. it's canvas coordination. (0,0) is top left. horizontal is y-axis. vertical is x-axis. start from the last block, reversely to the 1st block """ verts_ls = [] for i in range(no_of_blocks): block_start = start_ls[i] block_end = end_ls[i] verts = [[block_start, width/2.0+y], [block_start, -width/2.0+y], [block_end, -width/2.0+y], [block_end, width/2.0+y]] verts_ls.append(verts) PolyCollection.__init__(self, verts_ls, **kwargs)
def __init__(self, verts, *args, **kwargs):
'''
Create a Poly3DCollection.
*verts* should contain 3D coordinates.
Note that this class does a bit of magic with the _facecolors
and _edgecolors properties.
'''
PolyCollection.__init__(self, verts, *args, **kwargs)
self._zsort = 1
self._sort_zpos = None
def __init__(self, verts, *args, **kwargs):
'''
Create a Poly3DCollection.
*verts* should contain 3D coordinates.
Note that this class does a bit of magic with the _facecolors
and _edgecolors properties.
'''
PolyCollection.__init__(self, verts, *args, **kwargs)
self._zsort = 1
self._sort_zpos = None
def __init__(self, verts, *args, **kwargs):
'''
Create a Poly3DCollection.
*verts* should contain 3D coordinates.
Keyword arguments:
zsort, see set_zsort for options.
Note that this class does a bit of magic with the _facecolors
and _edgecolors properties.
'''
zsort = kwargs.pop('zsort', True)
PolyCollection.__init__(self, verts, *args, **kwargs)
self.set_zsort(zsort)
def __init__(self, map, mask, nest=False, **kwargs):
nside = healpix.npix2nside(len(mask))
self.v = pix2quad(nside, mask.nonzero()[0], nest)
PolyCollection.__init__(self, self.v, array=map[mask], **kwargs)
def __init__(self, map, mask, nest=False, **kwargs):
nside = healpix.npix2nside(len(mask))
self.v, ind = pix2quad(nside, mask.nonzero()[0], nest)
#print(len(ind), len(self.v), mask.sum())
PolyCollection.__init__(self, self.v, array=map[ind], **kwargs)
def __init__(self, map, mask, nest=False, **kwargs):
nside = healpix.npix2nside(len(mask))
self.v, ind = pix2quad(nside, mask.nonzero()[0], nest)
#print(len(ind), len(self.v), mask.sum())
PolyCollection.__init__(self, self.v, array=map[ind], **kwargs)
def __init__(self, annotated_box_ls, y=0, width=0.001, linewidths = None, box_line_widths = None,
colors = None,
antialiaseds = None,
linestyle = 'solid',
offsets = None,
transOffset = None,#transforms.identity_transform(),
norm = None,
cmap = None,
picker=False, pickradius=5, alpha=None, strand=None, facecolors=None, edgecolors=None, rotate_xy=False, \
**kwargs):
"""
2008-10-01
block_type='exon' has both facecolor and edgecolor red.
block_type='intron' has no facecolor and black edgecolor.
arguments edgecolors and facecolors in __init__() could overwrite the ones that generated based on the box_type.
2008-10-01
the annotated_box_ls is a list of (start, stop, box_type, is_translated, ...)
box_type = 'exon' or 'intron' and is_translated= 0 or 1. They are optional. Default is box_type ='intron', is_translated=0.
2008-09-26
linewidths controls the width of lines connecting exons or the arrow line, could be a list of floats of just one float.
box_line_widths controls the width of the boundaries of exon boxes
"""
#handle parameters for LineCollection
if linewidths is None:
linewidths = (mpl.rcParams['lines.linewidth'], )
if box_line_widths is None:
box_line_widths = (mpl.rcParams['lines.linewidth'], )
if colors is None:
colors = (mpl.rcParams['lines.color'], )
if antialiaseds is None:
antialiaseds = (mpl.rcParams['lines.antialiased'], )
self._colors = [
_colors.colorConverter.to_rgba(color, alpha) for color in colors
] #2008-10-26 use to_rgba() instead of to_rgba_list() because the latter is not present in matplotlib 0.98.3
self._aa = self._get_value(antialiaseds)
self._lw = self._get_value(linewidths)
self.set_linestyle(linestyle)
self._uniform_offsets = None
if offsets is not None:
offsets = asarray(offsets)
if len(offsets.shape) == 1:
offsets = offsets[numpy.newaxis, :] # Make it Nx2.
if transOffset is None:
if offsets is not None:
self._uniform_offsets = offsets
offsets = None
if hasattr(transforms, 'identity_transform'):
transOffset = transforms.identity_transform(
) #matplotlib 0.91.2
elif hasattr(transforms, 'IdentityTransform'):
transOffset = transforms.IdentityTransform(
) #matplotlib 0.98.3
self._offsets = offsets
self._transOffset = transOffset
self.pickradius = pickradius
#handle parameters for PolyCollection
verts_ls = []
segment_ls = []
no_of_blocks = len(annotated_box_ls)
verts_colors = []
_edgecolors = []
for i in range(no_of_blocks):
this_block = annotated_box_ls[i]
block_start, block_end = this_block[:2]
block_type = 'intron'
is_translated = 0
if len(this_block) >= 3:
block_type = this_block[2]
if len(this_block) >= 4:
is_translated = int(this_block[3])
if block_type == 'exon':
verts = [[block_start, width / 2.0 + y],
[block_start, -width / 2.0 + y],
[block_end, -width / 2.0 + y],
[block_end, width / 2.0 + y]]
if rotate_xy:
verts = [[row[1], row[0]] for row in verts]
verts_ls.append(verts)
if is_translated == 1:
verts_colors.append('r')
_edgecolors.append('r') #same edge color
else:
verts_colors.append('w') #no face color
_edgecolors.append('k')
else:
if rotate_xy:
segment_ls.append([(y, block_start), (y, block_end)])
else:
segment_ls.append([(block_start, y), (block_end, y)])
if not facecolors:
facecolors = verts_colors
if not edgecolors:
edgecolors = _edgecolors
#add an arrow
box_start = annotated_box_ls[0][0]
box_end = annotated_box_ls[-1][1]
if strand is not None:
arrow_length = abs(box_start - box_end) / 4
try:
strand = int(strand)
except:
pass
if strand == 1 or strand == 'plus':
arrow_offset = -arrow_length
arrow_end = box_end
elif strand == -1 or strand == 'minus':
arrow_offset = arrow_length
arrow_end = box_start
else: #can't tell which strand
arrow_offset = 0
arrow_end = box_end
if rotate_xy:
segment_ls.append([(y + width, arrow_end + arrow_offset),
(y + width / 2.0, arrow_end)])
else:
segment_ls.append([(arrow_end + arrow_offset, y + width),
(arrow_end, y + width / 2.0)])
self._segments = segment_ls
self.set_segments(segment_ls)
self._verts = verts
#self.set_alpha(alpha)
PolyCollection.__init__(self,
verts_ls,
linewidths=box_line_widths,
antialiaseds=antialiaseds,
edgecolors=edgecolors,
**kwargs)
self._facecolors = [
_colors.colorConverter.to_rgba(facecolor, alpha=alpha)
for facecolor in facecolors
] #in PolyCollection.__init__(), it doesn't handle alpha
self._picker = picker #to enable picker_event. PolyCollection's ancestor PatchCollection (collection.py) defines a method 'contains()'.
#Artist.pick() (in artist.py) calls pickable(), which checks self._picker, first to see whether this artist is pickable. then it calls picker() or contains().
self.update(kwargs)
def __init__(self, annotated_box_ls, y=0, width=0.001, linewidths = None, box_line_widths = None,
colors = None,
antialiaseds = None,
linestyle = 'solid',
offsets = None,
transOffset = None,#transforms.identity_transform(),
norm = None,
cmap = None,
picker=False, pickradius=5, alpha=None, strand=None, facecolors=None, edgecolors=None, rotate_xy=False, \
**kwargs):
"""
2008-10-01
block_type='exon' has both facecolor and edgecolor red.
block_type='intron' has no facecolor and black edgecolor.
arguments edgecolors and facecolors in __init__() could overwrite the ones that generated based on the box_type.
2008-10-01
the annotated_box_ls is a list of (start, stop, box_type, is_translated, ...)
box_type = 'exon' or 'intron' and is_translated= 0 or 1. They are optional. Default is box_type ='intron', is_translated=0.
2008-09-26
linewidths controls the width of lines connecting exons or the arrow line, could be a list of floats of just one float.
box_line_widths controls the width of the boundaries of exon boxes
"""
#handle parameters for LineCollection
if linewidths is None :
linewidths = (mpl.rcParams['lines.linewidth'], )
if box_line_widths is None :
box_line_widths = (mpl.rcParams['lines.linewidth'], )
if colors is None :
colors = (mpl.rcParams['lines.color'],)
if antialiaseds is None :
antialiaseds = (mpl.rcParams['lines.antialiased'], )
self._colors = [_colors.colorConverter.to_rgba(color, alpha) for color in colors] #2008-10-26 use to_rgba() instead of to_rgba_list() because the latter is not present in matplotlib 0.98.3
self._aa = self._get_value(antialiaseds)
self._lw = self._get_value(linewidths)
self.set_linestyle(linestyle)
self._uniform_offsets = None
if offsets is not None:
offsets = npy.asarray(offsets)
if len(offsets.shape) == 1:
offsets = offsets[npy.newaxis,:] # Make it Nx2.
if transOffset is None:
if offsets is not None:
self._uniform_offsets = offsets
offsets = None
if hasattr(transforms, 'identity_transform'):
transOffset = transforms.identity_transform() #matplotlib 0.91.2
elif hasattr(transforms, 'IdentityTransform'):
transOffset = transforms.IdentityTransform() #matplotlib 0.98.3
self._offsets = offsets
self._transOffset = transOffset
self.pickradius = pickradius
#handle parameters for PolyCollection
verts_ls = []
segment_ls = []
no_of_blocks = len(annotated_box_ls)
verts_colors = []
_edgecolors = []
for i in range(no_of_blocks):
this_block = annotated_box_ls[i]
block_start, block_end = this_block[:2]
block_type = 'intron'
is_translated = 0
if len(this_block)>=3:
block_type = this_block[2]
if len(this_block)>=4:
is_translated = int(this_block[3])
if block_type=='exon':
verts = [[block_start, width/2.0+y], [block_start, -width/2.0+y], [block_end, -width/2.0+y], [block_end, width/2.0+y]]
if rotate_xy:
verts = [[row[1], row[0]] for row in verts]
verts_ls.append(verts)
if is_translated==1:
verts_colors.append('r')
_edgecolors.append('r') #same edge color
else:
verts_colors.append('w') #no face color
_edgecolors.append('k')
else:
if rotate_xy:
segment_ls.append([(y, block_start), (y, block_end)])
else:
segment_ls.append([(block_start, y), (block_end,y)])
if not facecolors:
facecolors = verts_colors
if not edgecolors:
edgecolors = _edgecolors
#add an arrow
box_start = annotated_box_ls[0][0]
box_end = annotated_box_ls[-1][1]
if strand is not None:
arrow_length = abs(box_start-box_end)/4
try:
strand = int(strand)
except:
pass
if strand==1 or strand=='plus':
arrow_offset = -arrow_length
arrow_end = box_end
elif strand==-1 or strand=='minus':
arrow_offset = arrow_length
arrow_end = box_start
else: #can't tell which strand
arrow_offset = 0
arrow_end = box_end
if rotate_xy:
segment_ls.append([( y+width, arrow_end+arrow_offset), (y+width/2.0, arrow_end)])
else:
segment_ls.append([(arrow_end+arrow_offset, y+width), (arrow_end,y+width/2.0)])
self._segments = segment_ls
self.set_segments(segment_ls)
self._verts = verts
#self.set_alpha(alpha)
PolyCollection.__init__(self, verts_ls, linewidths=box_line_widths, antialiaseds=antialiaseds, edgecolors=edgecolors, **kwargs)
self._facecolors = [_colors.colorConverter.to_rgba(facecolor, alpha=alpha) for facecolor in facecolors] #in PolyCollection.__init__(), it doesn't handle alpha
self._picker = picker #to enable picker_event. PolyCollection's ancestor PatchCollection (collection.py) defines a method 'contains()'.
#Artist.pick() (in artist.py) calls pickable(), which checks self._picker, first to see whether this artist is pickable. then it calls picker() or contains().
self.update(kwargs)
