Plotting alignments

Alignments can be plotted using the BioBasket.plot_alignment() method.

>>> from sugar import read
>>> seqs = read('https://osf.io/download/j2wyv')
>>> seqs.plot_alignment(show=True, color='gray', figsize=(10, 4))
../_images/ali1.png 
>>> seqs[:, 70:120].plot_alignment(fname='ali.pdf', color=None, figsize=(10,8),
...                                symbols=True, aspect=2, alpha=0.5)
../_images/ali2.png

The following example shows an alignment of amino acids using the 'flower' color scheme, a color scheme that displays amino acids with a high BLOSSUM62 score in similar colors. Color schemes originate from Biotite (Gecos), Jalview and ClustalX, see here for an overview. The available color schemes are listed in get_color_scheme().

>>> seqs2 = seqs[:5, :150].copy()
>>> seqs2.translate(complete=True).plot_alignment(
...     show=True, color='flower', figsize=(10,8),  symbols=True,
...     aspect=2, alpha=0.5, edgecolors='w')
../_images/ali3.png

The plotting function has many options, including marking of plotting feature regions with different colors. Multi-line plots are not supported. If you need these, consider converting the sequences to a biotite Alignment object via seqs.tobiotite(msa=True) and using Biotite’s plotting capabilities.

Plotting features

Sugar can plot features with DNAFeaturesViewer. Use the plot_ftsviewer() method of FeatureList, BioBasket, or BioSeq.

Plot the features of the example sequence:

>>> from sugar import read
>>> seqs = read()
>>> seqs.plot_ftsviewer(show=True)
../_images/fts1.png

Here is another example of plotting the CDS features of an Ebolavirus RNA. The GenBank file is included in the provided tutorial files. It is downloaded again here using the Entrez client.

>>> from sugar.web import Entrez
>>> client = Entrez()
>>> seq = client.get_seq('AF086833')
>>> fts = seq.fts.select('cds')
>>> for ft in fts:
...    ft.meta.name = ft.meta._genbank.gene
>>> fts.plot_ftsviewer(colorby='name', seqlen=len(seq), figsize=(6, 2.5), show=True)
../_images/fts3.png

For comparison we plot all open reading frames with a minimum length of 500 nucleotides:

>>> orfs = seq.find_orfs(len_ge=500)
>>> orfs.plot_ftsviewer(colorby='rf', label=None, seqlen=len(seq), figsize=(6, 2.5), show=True)
../_images/fts4.png

Note

Use the colorby option to specify the category by which the features will be colored. Use the color argument to specify the colors used. See toftsviewer().

If you want more fine-grained control you can convert features to a GraphicRecord object with the toftsviewer() method and use the plotting method of the returned object:

>>> seqs = read()
>>> record = seqs[1].toftsviewer()
>>> record.plot()
../_images/fts2.png

Note

Using BioSeq or BioBasket.plot_ftsviewer() over FeatureList.plot_ftsviewer() has the advantage, that sequence lengths are used automatically.