lakeview.plot#

lakeview.plot.get_cmap_colors(cmap_name, format_='hex')#

Get all colors for a given matplotlib palette.

Adapted from https://gist.github.com/jdbcode/33d37999f950a36b43e058d15280b536.

>>> get_cmap_colors("Set2")
['#66c2a5', '#fc8d62', '#8da0cb', '#e78ac3', '#a6d854', '#ffd92f', '#e5c494', '#b3b3b3']
Parameters

  • cmap_name (str) –

  • format_ (Literal[('hex', 'rgb')]) –

Return type

list[Color]

lakeview.plot.get_random_colors(n, *, seed=0, cmap='hsv')#

Returns n random colors selected uniformly from cmap.

>>> get_random_colors(3)
[(0.0, 0.22463448382566054, 1.0, 1.0), (0.4018366371307548, 1.0, 0.0, 1.0), (1.0, 0.2316178786767022, 0.0, 1.0)]
Parameters

n (int) –

Return type

list[Color]

lakeview.plot.draw_rigid_polygon(ax, shape, position, position_transform, **kw)#

Draw a polygon patch with shape defined in inches and position defined in data, Axes or physical units.

Parameters
lakeview.plot.get_ax_size(ax)#

Return the size of a given Axes in inches.

>>> fig, ax = plt.subplots(figsize=(8, 6))
>>> get_ax_size(ax)
(6.2, 4.62)
Parameters

ax (matplotlib.axes._axes.Axes) –

lakeview.plot.scientific_notation(x, significant_figures=3, *, quote='$')#

Returns scientific notation in Matplotlib mathtext format.

>>> scientific_notation(0.000000013923, 4)
'$1.392\\times 10^{-8}$'
Parameters

  • x (float) –

  • significant_figures (int) –

  • quote (str) –

Return type

str

class lakeview.plot.PrunedMaxNLocator#

Bases: matplotlib.ticker.MaxNLocator

A Matplotlib tick locator that prunes ticks near the edge of the plot.

__init__(nbins=4, prune=(0.05, 0.05))#
Parameters

  • nbins (int) – Maximum number of intervals; one less than max number of ticks.

  • prune (tuple[float, float]) – A two-element tuple (prune_lower, prune_upper). Ticks outside the interval [vmin + prune_lower × (vmax - vmin), vmax - self._prune_upper × (vmax - vmin)] will be pruned. See PrunedMaxNLocator.tick_values().

tick_values(vmin, vmax)#

Return the values of the located ticks given vmin and vmax.

Note

To get tick locations with the vmin and vmax values defined automatically for the associated axis simply call the Locator instance:

>>> print(type(loc))
<type 'Locator'>
>>> print(loc())
[1, 2, 3, 4]
Parameters
class lakeview.plot.BasePairFormatter#

Bases: matplotlib.ticker.FuncFormatter

A Matplotlib tick formatter for common base pair units (bp, kb, Mb, Gb, Tb).

>>> formatter = BasePairFormatter('kb')
>>> formatter(24310)
'24.310 kb'
>>> formatter = BasePairFormatter('Mb', 2, show_suffix=False)
>>> formatter(844_293_192)
'844.29'
__init__(unit, decimals=None, *, show_suffix=True)#
Parameters

  • unit (BasePairUnit) – Base pair unit.

  • decimals (int | None) – The number of decimal places to show for the coefficient. The default is 0 for 'bp', or 3 for other values of unit.

  • show_suffix (bool) – Whether to show the unit as a suffix.

classmethod from_limits(limits, *, show_suffix=True)#

Automatically select reasonable unit and decimals based on axes limits.

>>> fig, ax = plt.subplots()
>>> ax.set_xlim(3200000, 5840000)
(3200000.0, 5840000.0)
>>> formatter = BasePairFormatter.from_limits(ax.get_xlim())
>>> formatter
BasePairFormatter(unit='Mb', decimals=1, show_suffix=True)
>>> ax.xaxis.set_major_formatter(formatter)
Parameters