pybedtools.contrib.plotting.BedToolsDemo

class pybedtools.contrib.plotting.BedToolsDemo(config, method, data_path=None, result_kwargs=None, method_kwargs=None, title_kwargs=None, new_style=True, subplots_adjust=None, *args, **kwargs)[source]
__init__(config, method, data_path=None, result_kwargs=None, method_kwargs=None, title_kwargs=None, new_style=True, subplots_adjust=None, *args, **kwargs)[source]

Class to handle BEDTools demos in a way that maintains flexibility.

If the config list contains only one item, assume the method is one of the “-i” tools that only operate on one file.

If the config list contains two items, then use the first as “-a” and the second as “-b”.

Parameters:

  • config – Either a list of (filename, options) tuples – see docstring for TrackCollection for more info.

  • method – Method of BedTool object to use, e.g., ‘intersect’

  • data_path – If not None, this path will be prepended to the files listed in config

  • result_kwargs – Configuration for the results track. This isn’t added to the config list because the results haven’t been created yet…

  • method_kwargs – Keyword argument that are passed to the method, e.g., u=True

  • title_kwargs – Keyword args for plot title (the text itself will come from the command that was run; this is for things like font size)

  • new_style – Edit commands so that they use the “new style” BEDTools calls (“bedtools intersect” rather than “intersectBed”)

  • subplots_adjust – Additional kwargs sent to the figure’s subplots_adjust() method, e.g., dict(top=0.7)

  • args – Addtional arguments sent to TrackCollection

  • kwargs – Additional keyword arguments sent to TrackCollection

Methods

__init__(config, method[, data_path, ...])

Class to handle BEDTools demos in a way that maintains flexibility.

plot([ax])

If ax is None, create a new figure.