biotite.sequence.graphics.LetterSimilarityPlotter

class biotite.sequence.graphics.LetterSimilarityPlotter(axes, matrix=None, color_symbols=False, font_size=None, font_param=None)

Bases: LetterPlotter

This SymbolPlotter colors the symbols based on the similarity with the other symbols in the same column.

The color intensity (or colormap value, respectively) of a symbol scales with similarity of the respective symbol to the other symbols in the same alignment column.

Parameters

axesAxes

A Matplotlib axes, that is used as plotting area.

matrixSubstitutionMatrix, optional

The substitution matrix to use the similarity scores from. By default the normalized similarity is 1 for identity and 0 for non-identity.

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.

Notes

For determination of the color, this a measure called average normalized similarity is used.

The normalized similarity of one symbol a to another symbol b (both in aphabet X) is defined as

\[S_{norm}(a,b) = \frac{S(a,b) - \min\limits_x(S(a,x))} {\max\limits_x(S(a,x)) - \min\limits_x(S(a,x))}\]

\[a,b,x \in X\]

where S(x,y) is the similarity score of the two symbols x and y described in the substitution matrix. The similarity S(x,-) is always 0. As the normalization is conducted only with respect to a, the normalized similarity is not commutative.

The average normalized similarity of a symbol a is determined by averaging the normalized similarity over each symbol b_i in the same alignment column.

\[S_{norm,av}(a) = \frac{1}{n-1} \left[\left(\sum\limits_{i=1}^n S_{norm}(a,b_i)\right) - S_{norm}(a,a)\right]\]

The normalized similarity of a to itself is subtracted, because a does also occur in b_i.

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.

set_color(color=None, cmap=None)

Set the alignemnt colors used for plotting.

This function takes either a color or a colormap.

Parameters

colortuple or str, optional

A Matplotlib compatible color. If this parameter is given, the box color in an interpolated value between white and the given color, or, if color_symbols is set, between the given color and black. The interpolation percentage is given by the normalized similarity.

cmapColormap, optional

The boxes (or symbols, if color_symbols is set) are colored based on the normalized similarity value on the given Colormap.