Skip to content

Plot Style

This module provides opt-in Nature-journal-style formatting for dot-explorer plots: Helvetica/Arial fonts at 5–7 pt, 0.5 pt line and axes widths, no top/right spines, outward ticks, and 300 dpi tight-bbox figure export defaults.

Use the context manager to style a single plot:

from dot_explorer import DotPlotter, SequenceIndex, nature_style

idx = SequenceIndex(k=10)
idx.add_sequence("seq1", "ACGTACGTACGTACGTACGT")
idx.add_sequence("seq2", "TACGTACGTACGTACGTACG")

plotter = DotPlotter(idx)
with nature_style():
    fig = plotter.plot(output_path="dotplot.png", dpi=300)

Note

Explicit keyword arguments always override rcParams, and DotPlotter.plot passes its own dpi argument (default 150) to savefig. Pass dpi=300 explicitly, as above, to save at Nature's recommended resolution; the savefig.dpi/savefig.bbox defaults in the style apply to plain plt.savefig() calls that omit those arguments.

Or apply the style globally for the session:

from dot_explorer import use_nature_style

use_nature_style()

Constants

NATURE_RC = {'font.family': 'sans-serif', 'font.sans-serif': ['Helvetica', 'Arial', 'Helvetica Neue', 'Liberation Sans', 'Nimbus Sans', 'DejaVu Sans'], 'font.size': 7.0, 'axes.titlesize': 7.0, 'axes.labelsize': 7.0, 'xtick.labelsize': 6.0, 'ytick.labelsize': 6.0, 'legend.fontsize': 6.0, 'legend.title_fontsize': 7.0, 'figure.titlesize': 7.0, 'lines.linewidth': 0.5, 'axes.linewidth': 0.5, 'grid.linewidth': 0.5, 'patch.linewidth': 0.5, 'xtick.major.width': 0.5, 'ytick.major.width': 0.5, 'xtick.minor.width': 0.5, 'ytick.minor.width': 0.5, 'axes.spines.top': False, 'axes.spines.right': False, 'xtick.direction': 'out', 'ytick.direction': 'out', 'savefig.dpi': 300, 'savefig.bbox': 'tight'} module-attribute

rcParams implementing Nature journal figure-formatting guidelines.

Keys mirror :data:matplotlib.rcParams: Helvetica/Arial sans-serif fonts at 5-7 pt, 0.5 pt line and axes widths, no top/right spines, outward ticks, and 300 dpi tight-bbox savefig defaults.

Functions

nature_style()

Return a context manager that applies the Nature style temporarily.

Inside the with block :data:matplotlib.rcParams reflects :data:NATURE_RC; on exit the previous rcParams are restored, even if an exception was raised.

Returns:

Type Description
AbstractContextManager

A :func:matplotlib.rc_context context manager configured with :data:NATURE_RC.

Examples:

>>> import matplotlib
>>> from dot_explorer.style import nature_style
>>> with nature_style():
...     assert matplotlib.rcParams['savefig.dpi'] == 300
Source code in dot_explorer/style.py 
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
def nature_style() -> AbstractContextManager[None]:
    """Return a context manager that applies the Nature style temporarily.

    Inside the ``with`` block :data:`matplotlib.rcParams` reflects
    :data:`NATURE_RC`; on exit the previous rcParams are restored,
    even if an exception was raised.

    Returns
    -------
    contextlib.AbstractContextManager
        A :func:`matplotlib.rc_context` context manager configured with
        :data:`NATURE_RC`.

    Examples
    --------
    >>> import matplotlib
    >>> from dot_explorer.style import nature_style
    >>> with nature_style():
    ...     assert matplotlib.rcParams['savefig.dpi'] == 300
    """
    # Cast: matplotlib stubs key rc dicts by a Literal of every rcParam name,
    # which a dict[str, Any] constant cannot satisfy directly.
    return matplotlib.rc_context(rc=cast('dict[Any, Any]', NATURE_RC))

use_nature_style()

Apply the Nature style globally to :data:matplotlib.rcParams.

Unlike :func:nature_style, the change persists for the rest of the session (or until rcParams are reset, e.g. via :func:matplotlib.rcdefaults).

Returns:

Type Description
None

This function mutates :data:matplotlib.rcParams in place.

Examples:

>>> import matplotlib
>>> from dot_explorer.style import use_nature_style
>>> use_nature_style()
>>> matplotlib.rcParams['axes.spines.top']
False
>>> matplotlib.rcdefaults()  # reset to matplotlib library defaults
Source code in dot_explorer/style.py 
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
def use_nature_style() -> None:
    """Apply the Nature style globally to :data:`matplotlib.rcParams`.

    Unlike :func:`nature_style`, the change persists for the rest of the
    session (or until rcParams are reset, e.g. via
    :func:`matplotlib.rcdefaults`).

    Returns
    -------
    None
        This function mutates :data:`matplotlib.rcParams` in place.

    Examples
    --------
    >>> import matplotlib
    >>> from dot_explorer.style import use_nature_style
    >>> use_nature_style()
    >>> matplotlib.rcParams['axes.spines.top']
    False
    >>> matplotlib.rcdefaults()  # reset to matplotlib library defaults
    """
    matplotlib.rcParams.update(cast('dict[Any, Any]', NATURE_RC))