def update_ticks(axes, coord, components, is_log):
"""
Changes the axes to have the proper tick formatting based on the type of
component.
Returns `None` or the number of categories if components is Categorical.
Parameters
----------
axes : `~matplotlib.axes.Axes`
A matplotlib axis object to alter
coord : { 'x' | 'y' }
The coordinate axis on which to update the ticks
components : iterable
A list of components that are plotted along this axis
if_log : boolean
Whether the axis has a log-scale
"""
if coord == 'x':
axis = axes.xaxis
elif coord == 'y':
axis = axes.yaxis
else:
raise TypeError("coord must be one of x,y")
is_cat = any(comp.categorical for comp in components)
is_date = any(comp.datetime for comp in components)
if is_date:
loc = AutoDateLocator()
fmt = AutoDateFormatter(loc)
axis.set_major_locator(loc)
axis.set_major_formatter(fmt)
elif is_log:
axis.set_major_locator(LogLocator())
axis.set_major_formatter(LogFormatterMathtext())
elif is_cat:
all_categories = np.empty((0,), dtype=np.object)
for comp in components:
all_categories = np.union1d(comp.categories, all_categories)
locator = MaxNLocator(10, integer=True)
locator.view_limits(0, all_categories.shape[0])
format_func = partial(tick_linker, all_categories)
formatter = FuncFormatter(format_func)
axis.set_major_locator(locator)
axis.set_major_formatter(formatter)
return all_categories.shape[0]
else:
axis.set_major_locator(AutoLocator())
axis.set_major_formatter(ScalarFormatter())
def update_ticks(axes, coord, components, is_log):
"""
Changes the axes to have the proper tick formatting based on the type of
component.
:param axes: A matplotlib axis object to alter
:param coord: 'x' or 'y'
:param components: A list() of components that are plotted along this axis
:param is_log: Boolean for log-scale.
:kwarg max_categories: The maximum number of categories to display.
:return: None or #categories if components is Categorical
"""
if coord == 'x':
axis = axes.xaxis
elif coord == 'y':
axis = axes.yaxis
else:
raise TypeError("coord must be one of x,y")
is_cat = all(comp.categorical for comp in components)
if is_log:
axis.set_major_locator(LogLocator())
axis.set_major_formatter(LogFormatterMathtext())
elif is_cat:
all_categories = np.empty((0,), dtype=np.object)
for comp in components:
all_categories = np.union1d(comp.categories, all_categories)
locator = MaxNLocator(10, integer=True)
locator.view_limits(0, all_categories.shape[0])
format_func = partial(tick_linker, all_categories)
formatter = FuncFormatter(format_func)
axis.set_major_locator(locator)
axis.set_major_formatter(formatter)
return all_categories.shape[0]
else:
axis.set_major_locator(AutoLocator())
axis.set_major_formatter(ScalarFormatter())
else:
fig = plotG_one(n-1, r, clens, drawraw=args.drawraw,rawcolor=rawclr,
smoothcolor=smoothclr, smoothwidth=smoothwidth,
maxgap=args.maxgap)
if args.maxmin:
fillbetween_chrom(r.coords[n-1], r.maxminG[n-1], maxgap=args.maxgap, alpha=0.5)
ax = fig.gca()
if 'coords' in vars(args):
ax.set_xlim(*args.coords)
if n > 0:
if 'nticks' in vars(args):
m = MaxNLocator(*args.nticks)
m.view_limits(*ax.get_xlim())
ax.xaxis.set_major_locator(m)
else:
ax.xaxis.set_major_locator(MaxNLocator(4))
if 'ylim' in vars(args):
ax.set_ylim(*args.ylim)
if 'figsize' in vars(args):
fig.set_size_inches(*args.figsize)
if args.threshold > 0:
ax.hlines(args.threshold, 0, tlen, color=args.thresholdclr, linestyle='dashed')
name,ext = os.path.splitext(args.outfile)
# check extension of outfile
if ext in ('.png','.pdf','.jpg','.ps','.eps','.svg'):
def update_ticks(axes, coord, kinds, is_log, categories, projection='rectilinear', radians=True, label=None):
"""
Changes the axes to have the proper tick formatting based on the type of
component.
Returns `None` or the number of categories if components is Categorical.
Parameters
----------
axes : :class:`matplotlib.axes.Axes`
A matplotlib axis object to alter
coord : { 'x' | 'y' }
The coordinate axis on which to update the ticks
components : iterable
A list of components that are plotted along this axis
if_log : boolean
Whether the axis has a log-scale
projection: str
The name of the matplotlib projection for the axes object. Defaults to 'rectilinear'.
Currently only the scatter viewer supports different projections.
"""
# Short circuit the full-sphere projections
if projection in ['aitoff', 'hammer', 'mollweide', 'lambert']:
return
if coord == 'x':
axis = axes.xaxis
elif coord == 'y':
axis = axes.yaxis
else:
raise TypeError("coord must be one of x,y")
is_cat = 'categorical' in kinds
is_date = 'datetime' in kinds
if is_date:
loc = AutoDateLocator()
fmt = AutoDateFormatter(loc)
axis.set_major_locator(loc)
axis.set_major_formatter(fmt)
elif is_log:
axis.set_major_locator(LogLocator())
axis.set_major_formatter(LogFormatterMathtext())
elif is_cat:
locator = MaxNLocator(10, integer=True)
locator.view_limits(0, categories.shape[0])
format_func = partial(tick_linker, categories)
formatter = FuncFormatter(format_func)
axis.set_major_locator(locator)
axis.set_major_formatter(formatter)
# Have to treat the axes for polar plots differently
elif projection == 'polar':
if coord == 'x':
axis.set_major_locator(ThetaLocator(AutoLocator()))
formatter_type = ThetaRadianFormatter if radians else ThetaDegreeFormatter
axis.set_major_formatter(formatter_type(label))
for lbl, loc in zip(axis.get_majorticklabels(), axis.get_majorticklocs()):
lbl.set_horizontalalignment(polar_tick_alignment(loc, radians))
else:
axis.set_major_locator(AutoLocator())
axis.set_major_formatter(PolarRadiusFormatter(label))
for lbl in axis.get_majorticklabels():
lbl.set_fontstyle("italic")
else:
axis.set_major_locator(AutoLocator())
axis.set_major_formatter(ScalarFormatter())
if n <= 0:
fig = plotG_all(r, clens, drawraw=args.drawraw,rawcolor=rawclr,
smoothcolor=smoothclr, smoothwidth=smoothwidth,
maxgap=args.maxgap)
else:
fig = plotG_one(n-1, r, clens, drawraw=args.drawraw,rawcolor=rawclr,
smoothcolor=smoothclr, smoothwidth=smoothwidth,
maxgap=args.maxgap)
ax = fig.gca()
if 'coords' in vars(args):
ax.set_xlim(*args.coords)
if n > 0:
if 'nticks' in vars(args):
m = MaxNLocator(*args.nticks)
m.view_limits(*ax.get_xlim())
ax.xaxis.set_major_locator(m)
else:
ax.xaxis.set_major_locator(MaxNLocator(4))
if 'ylim' in vars(args):
ax.set_ylim(*args.ylim)
if 'figsize' in vars(args):
fig.set_size_inches(*args.figsize)
if args.threshold > 0:
ax.hlines(args.threshold, 0, tlen, color=args.thresholdclr, linestyle='dashed')
name,ext = os.path.splitext(args.outfile.name)
# check extension of outfile
if ext in ('.png','.pdf','.jpg','.ps','.eps','.svg'):
