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mach2.SolutionSet

(back)

Object containg a set of solutions (a refined phylogeny and a migration graph). This is returned by mach2.MACH.solve.

Constructor

mach2.SolutionSet(sol_list)

Parameters

  • sol_list (list[tuple[mach2.RefinedPhylogeny, mach2.MigrationGraph]]): The list of solutions to PMH-TR.

Methods

__len__()

In order to get the number of solutions, use len(solutions)

__getitem__(key)

To index into a solution, use solutions[key]

co_occurence_table() (pandas.DataFrame)

Returns a heatmap of the frequency of migrations that were in co-migrations together.

compute_summary(primary=None) (collections.defaultdict)

Returns a summary migration graph, unioning edges across the solutions.

Parameters

  • primary (str): Specify a primary argument if you would like to constrain solutions from a single primary tumor location.

summary(self, primary=None, colormap=None, colormap_file=None, consider_multi_edges=False, dot=True) (graphviz.DiGraph | collections.defaultdict)

A packaged method that either returns a DOT visualization of the summary graph, or the dictionary representing a summary graph.

Parameters

  • primary (str): Specify a primary argument if you would like to constrain solutions from a single primary tumor location.
  • colormap (dict[str, int]): A mapping between anatomic label to color index
  • colormap_file (str): The coloring file, if a file is being passed instead of colormap data
  • consider_multi_edges (bool): Also union parallel edges that distinguish migration events at different times, but from the same locations
  • dot (bool): Return a dot visualization, and not a dictionary. If False, a collections.defaultdict will be returned.

summary_dot(filename, primary=None, colormap=None, colormap_file=None, consider_multi_edges=False)

Returns a DOT visualization of the summary graph

Parameters

  • filename (str): The name of the file being written to
  • primary (str): Specify a primary argument if you would like to constrain solutions from a single primary tumor location.
  • colormap (dict[str, int]): A mapping between anatomic label to color index
  • colormap_file (str): The coloring file, if a file is being passed instead of colormap data
  • consider_multi_edges (bool): Also union parallel edges that distinguish migration events at different times, but from the same locations

json(name='') (dict)

Returns a json object representing the solutions returned.

Parameters

  • name (str): Name of the solution set returned. Ex. patient1

write_json(name='', filename=None)

Write json object representing the solutions returned to file

Parameters

  • name (str): Name of the solution set returned. Ex. patient1
  • filename (str): The name of the file being written to

open_in_viz()

Open the solution space in MACH2-Viz