`LetterTypePlotter`#

class biotite.sequence.graphics.LetterTypePlotter(axes: Axes, alphabet: Any, color_scheme: str | list[Any] | None = None, color_symbols: bool = False, font_size: float | None = None, font_param: dict[str, Any] | None = None)[source]#

Bases: LetterPlotter

This SymbolPloter colors each symbol based on the general color of that symbol defined by a color scheme.

EXPERIMENTAL: Future API changes are probable.

Parameters:

axesAxes: A Matplotlib axes, that is used as plotting area.
alphabetAlphabet: The alphabet of the alignment(s) to be plotted.
color_schemestr or list of (tuple or str), optional: Either a valid color scheme name (e.g. "flower", "clustalx", blossom, etc.) or a list of Matplotlib compatible colors. The list length must be at least as long as the length of the alphabet used by the sequences.
color_symbolsbool, optional: If true, the symbols themselves are colored. If false, the symbols are black, and the boxes behind the symbols are colored.
font_sizefloat, optional: Font size of the sequence symbols.
font_paramdict, optional: Additional parameters that is given to the matplotlib.Text instance of each symbol.

get_color(alignment: Alignment, column_i: int, seq_i: int) → Any#

Get the color of a symbol at a specified position in the alignment.

The symbol is specified as position in the alignment’s trace (trace[pos_i, seq_i]).

PROTECTED: Override when inheriting.

Parameters:

alignmentAlignment: The respective alignment.
column_iint: The position index in the trace.
seq_iint: The sequence index in the trace.

Returns:

colorobject: A Matplotlib compatible color used for the background or the symbol itself at the specifed position.

plot_symbol(bbox: Bbox, alignment: Alignment, column_i: int, seq_i: int) → None#

Get the color of a symbol at a specified position in the alignment.

The symbol is specified as position in the alignment’s trace (trace[pos_i, seq_i]).

Parameters:

bboxBbox: The axes area to plot the symbol in.
alignmentAlignment: The respective alignment.
column_iint: The position index in the trace.
seq_iint: The sequence index in the trace.

LetterTypePlotter#

`LetterTypePlotter`#