biotite.sequence.graphics¶

A subpackage for visualization of sequence related objects.

The visualizations make use of Matplotlib for plotting. Therefore, each plotting function requires an Axes object, where the visualization should be performed.

The resulting plots are customizable: Labels, location numbers, etc. are usually placed into the axes tick labels, making tham accessible for modification via the usual Matplotlib API. Some aspects of the plotting itself are also customizable: For example the plot_alignment() function uses a interchangable SymbolPlotter, that knows how to draw the symbols of an alignment. Similarily, the appearance of sequence features in the function plot_feature_map() is customized via FeaturePlotter objects.

Plotting functions¶

`plot_feature_map`	Plot a sequence annotation, by showing the range of each feature on one or multiple position depicting line(s).
`plot_sequence_logo`	Create a sequence logo.
`plot_alignment`	Plot a pairwise or multiple sequence alignment.
`plot_alignment_similarity_based`	Plot a pairwise or multiple sequence alignment highlighting the similarity per alignment column.
`plot_alignment_type_based`	Plot a pairwise or multiple sequence alignment coloring each symbol based on the symbol type.
`plot_dendrogram`	Plot a dendrogram from a (phylogenetic) tree.

Symbol plotters¶

`SymbolPlotter`	Subclasses of this abstract base class define how symbols in an alignment are drawn onto an `Axes` object.
`LetterPlotter`	This abstract `SymbolPlotter` is the most widely used one.
`LetterSimilarityPlotter`	This `SymbolPlotter` colors the symbols based on the similarity with the other symbols in the same column.
`LetterTypePlotter`	This SymbolPloter colors each symbol based on the general color of that symbol defined by a color scheme.

Feature plotters¶

`FeaturePlotter`	A `FeaturePlotter` is an object, that 'knows' how to draw a certain type of sequence feature onto a `matplotlib.Axes`.
`CodingPlotter`	A plotter for the CDS and gene features.
`PromoterPlotter`	A plotter for regulatory features with the promoter or TATA_box class.
`TerminatorPlotter`	A plotter for regulatory features with the terminator class.
`RBSPlotter`	A plotter for regulatory features with the ribosome_binding_site class.
`MiscFeaturePlotter`	A plotter that matches any feature.

Color schemes¶

`load_color_scheme`	Load a color scheme from a JSON file.
`get_color_scheme`	Get a color scheme by name and alphabet.
`list_color_scheme_names`	Get a list of available color scheme names for a given alphabet.

Miscellaneous¶

`ArrayPlotter`	This `SymbolPlotter` quantitatively decorates sequences alignments, with molecular recognition data obtained from e.g.
`plot_alignment_array`	Plot a pairwise sequence alignment using an `ArrayPlotter` instance.
`plot_plasmid_map`	Plot a plasmid map using the sequence features in the given `Annotation`.