biotite.sequence.graphics.ArrayPlotter

class biotite.sequence.graphics.ArrayPlotter(axes, fl_score, color_symbols=False, font_size=None, font_param=None)[source]

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()
get_color(alignment, column_i, seq_i)

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, alignment, column_i, seq_i)

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.