biotite.sequence.graphics.plot_alignment_type_based

biotite.sequence.graphics.plot_alignment_type_based(axes, alignment, symbols_per_line=50, show_numbers=False, number_size=None, number_functions=None, labels=None, label_size=None, show_line_position=False, spacing=1, color_scheme=None, color_symbols=False, symbol_size=None, symbol_param=None, symbol_spacing=None)[source]

Plot a pairwise or multiple sequence alignment coloring each symbol based on the symbol type.

This function works like plot_alignment() with a SymbolPlotter, that colors the symbols based on a color scheme. 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.

alignmentAlignment

The pairwise or multiple sequence alignment to be plotted. The alphabet of each sequence in the alignment must be the same.

symbol_plotterSymbolPlotter

Defines how the symbols in the alignment are drawn.

symbols_per_lineint, optional

The amount of alignment columns that are diplayed per line.

show_numbersbool, optional

If true, the sequence position of the symbols in the last alignment column of a line is shown on the right side of the plot. If the last symbol is a gap, the position of the last actual symbol before this gap is taken. If the first symbol did not occur up to this point, no number is shown for this line. By default the first symbol of a sequence has the position 1, but this behavior can be changed using the number_functions parameter.

number_sizefloat, optional

The font size of the position numbers

number_functionslist of [(None or Callable(int -> int)], optional

By default the position of the first symbol in a sequence is 1, i.e. the sequence position is the sequence index incremented by 1. The behavior can be changed with this parameter: If supplied, the length of the list must match the number of sequences in the alignment. Every entry is a function that maps a sequence index (int) to a sequence position (int) for the respective sequence. A None entry means, that the default numbering is applied for the sequence.

labelslist of str, optional

The sequence labels. Must be the same size and order as the sequences in the alignment.

label_sizefloat, optional

Font size of the labels

show_line_positionbool, optional

If true the position within a line is plotted below the alignment.

spacingfloat, optional

The spacing between the alignment lines. 1.0 means that the size is equal to the size of a symbol box.

color_schemestr or list of (tuple or str), optional

Either a valid color scheme name (e.g. "rainbow", "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.

symbol_sizefloat, optional

Font size of the sequence symbols.

symbol_paramdict

Additional parameters that is given to the matplotlib.Text instance of each symbol.

symbol_spacingint, optional

А space is placed between each number of elements desired by variable.