ArrayPlotter

class biotite.sequence.graphics.ArrayPlotter(axes: Axes, fl_score: ndarray[tuple[K, N], dtype[floating]], color_symbols: bool = False, font_size: float | None = None, font_param: dict[str, Any] | None = None)

Bases: LetterPlotter

This SymbolPlotter quantitatively decorates sequences alignments, with molecular recognition data obtained from e.g. microarrays. Symbols are visualized as characters on a colored background box. The color of a given box represents the recognition signal. The intensity of the color, is proportional to the strenght of the recognition.

Parameters:

axesAxes

A Matplotlib axes, that is used as plotting area.

fl_scorenumpy.ndarray

The ndarray to store recognition values corresponding to the score residues. By default, the normalized score is 1 for maximum recognition and 0 for non-recognition (no color).

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_cmap() → Any

get_color(alignment: Alignment, column_i: int, seq_i: int) → tuple[float, float, float, float]

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.

Gallery

Plot epitope mapping data onto protein sequence alignments

Plot epitope mapping data onto protein sequence alignments