colors

Utilities for manipulating colors.

BNF

<sequence-color-spec> ::=
    {
        "A": <color-spec>,
        "C": <color-spec>,
        "G": <color-spec>,
        "T": <color-spec>
    }
<color-spec> ::=
    {"rgb": [<number>, <number>, <number>]}
  | {"rgba": [<number>, <number>, <number>, <number>]}
  | {"tol": <integer>}
  | {"tol-light": <integer>}
  | {"ibm": <integer>}
  | {"wong": <integer>}
  | [<number>, <number>, <number>«, <number>»]
<list-of-sequence-color-spec> ::=
    <sequence-color-spec>«, <list-of-sequence-color-spec>»
<list-of-color-spec> ::=
    <color-spec>«, <list-of-color-spec>»
bpreveal.colors.tol: tuple[tuple[float, float, float] | tuple[float, float, float, float], ...]

The muted color scheme by Paul Tol.

../_images/tol.png
Type:

tuple[RGB_T, …]

bpreveal.colors.ibm: tuple[tuple[float, float, float] | tuple[float, float, float, float], ...]

The IBM design library’s color blind palette.

../_images/ibm.png
Type:

tuple[RGB_T, …]

bpreveal.colors.wong: tuple[tuple[float, float, float] | tuple[float, float, float, float], ...]

Bang Wong’s palette. Used for DNA.

../_images/wong.png
Type:

tuple[RGB_T, …]

bpreveal.colors.tolLight: tuple[tuple[float, float, float] | tuple[float, float, float, float], ...]

The light color scheme by Paul Tol, but with light blue and olive deleted.

../_images/tolLight.png
Type:

tuple[RGB_T, …]

bpreveal.colors.dnaWong: DNA_COLOR_SPEC_T = {'A': {'wong': 3}, 'C': {'wong': 5}, 'G': {'wong': 4}, 'T': {'wong': 6}}

The default color map for DNA bases.

A is green, C is blue, G is yellow, and T is red.

bpreveal.colors.defaultProfile: dict[Literal['rgb'], tuple[float, float, float]] | dict[Literal['rgba'], tuple[float, float, float, float]] | dict[Literal['tol'], int] | dict[Literal['tol-light'], int] | dict[Literal['ibm'], int] | dict[Literal['wong'], int] | tuple[float, float, float] | tuple[float, float, float, float]

The default color for profile plots. It’s tol[0].

Type:

COLOR_SPEC_T

bpreveal.colors.pisaClip = <matplotlib.colors.ListedColormap object>

The color map used for PISA plots, including green and pink clipping colors.

../_images/pisaClip.png
bpreveal.colors.pisaNoClip = <matplotlib.colors.ListedColormap object>

The color map for PISA plots but without the clipping warning colors.

../_images/pisaNoClip.png
bpreveal.colors.parseSpec(colorSpec)

Given a color-spec (See the BNF), convert it into an rgb or rgba tuple.

Parameters:

colorSpec (COLOR_SPEC_T | str) – The color specification.

Returns:

An rgb triple (or rgba quadruple).

Return type:

tuple[float, float, float] | tuple[float, float, float, float]

Based on the shape of colorSpec, this function interprets it differently. If colorSpec is a…

3-tuple

it is interpreted as an rgb color,

4-tuple

it is interpreted as rgba,

{"rgb": (0.1, 0.2, 0.3)}

it is interpreted as an rgb color,

{"rgba": (0.1, 0.2, 0.3, 0.8)}

it is interpreted as an rgba color,

{"<palette-name>": 3}

where <palette-name> is one of “tol”, “tol-light”, “wong”, or “ibm”), then the value is the color i in the corresponding palette.

"b"

or any other string, then it is interpreted as a matplotlib color string and is passed to matplotlib.colors.to_rgb.

bpreveal.colors.loadFonts()

Configures the matplotlib default fonts to be in the Libertinus family.

This places Libertinus fonts at the top of the order for serif and sans-serif fontfamily, but does not overwrite the monospace family.

Return type:

None