plot_alignment_array
#
- biotite.sequence.graphics.plot_alignment_array(axes, alignment, fl_score, 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=None, cmap=None, symbol_spacing=None, symbol_size=None, symbol_param=None)[source]#
Plot a pairwise sequence alignment using an
ArrayPlotter
instance.Highlights sequence recognition regions at the positions of the respective score residue per alignment column.
- Parameters:
- axesAxes
A Matplotlib axes, that is used as plotting area.
- alignmentAlignment
The pairwise sequence alignment to be plotted.
- fl_scorendarray
The array to map fluorescence values to score residues. By default the normalized score is 1 for maximum recognition and 0 for non-recognition (no color).
- symbol_plotterSymbolPlotter
Instance of ArrayPlotter. Defines how the symbols are drawn in the alignment.
- symbols_per_lineint, optional
The amount of alignment columns that are displayed 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.
- colortuple or str, optional
A Matplotlib compatible color.
- cmapColormap or str, optional
The boxes are colored based on the normalized intensity value on the given Matplotlib Colormap.
- 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
A space is placed between each number of elements desired by variable.
Notes
A ‘*’ represents a sequence match on the alignment A ‘-’ represents a sequence gap on the alignment
Gallery#

Plot epitope mapping data onto protein sequence alignments