¶

tree_set¶

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tree_set(
   file, output_file = None, distance_matrix = None, metadata = None
)

Class for the analysis of a set of phylogenetic trees

Methods:

.calculate_distances¶

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.calculate_distances(
   method
)

Computes tree_set distance matrix with method of choice

Args

• method (str) : method/algorithm used to compute distance matrix

.embed¶

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.embed(
   method, dimensions, quality = False, report = False
)

Compute embedding with n-dimensions and method of choice

Args

• method (str) : method of choice to embed data
• dimensions (type) : number of dimensions/components
• quality (bool, optional) : returns quality report and self.emb_quality. Defaults to False.

.plot_2D¶

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.plot_2D(
   method, save = False, name_plot = None, static = False, plot_meta = 'SET-ID',
   plot_set = None, select = False, same_scale = False
)

Plot 2D embedding performed with method of choice

Args

• method (str) : embedding method
• save (bool, optional) : save plot HTML. Defaults to False.
• name_plot (str, optional) : name of plot's file. Defaults to None.
• static (bool, optional) : return less interactive plot. Defaults to False.
• plot_meta (str, optional) : meta-variale used to color the points. Defaults to "SET-ID".
• plot_set (list, optional) : list of sets to plot from set_collection. Defaults to None.
• select (bool, optional) : return set of buttons to show or hide specific traces. Defaults to False.
• same_scale (bool, optional) : use same color_scale for all traces when scale is continuous. Defaults to False.

Raises

• ValueError : method can only be either pcoa or tsne for now

Returns

• plot : either interactive or not

.plot_3D¶

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.plot_3D(
   method, save = False, name_plot = None, static = False, plot_meta = 'SET-ID',
   plot_set = None, select = False, same_scale = False, z_axis = None
)

Plot 3D embedding performed with method of choice

Args

• method (str) : embedding method
• save (bool, optional) : save plot HTML. Defaults to False.
• name_plot (str, optional) : name of plot's file. Defaults to None.
• static (bool, optional) : return less interactive plot. Defaults to False.
• plot_meta (str, optional) : meta-variale used to color the points. Defaults to "SET-ID".
• plot_set (list, optional) : list of sets to plot from set_collection. Defaults to None.
• select (bool, optional) : return set of buttons to show or hide specific traces. Defaults to False.
• same_scale (bool, optional) : use same color_scale for all traces when scale is continuous. Defaults to False.

Raises

• ValueError : method can only be either pcoa or tsne for now

Returns

• plot : either interactive or not

.get_subset¶

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.get_subset(
   n_required, method = 'sequence'
)

Gets subset of phylogenetic trees

Args

• n_required (int) : number of points to extract
• method (str, optional) : method used to extact points ('sequence', 'random', 'syst'). Defaults to "sequence".

Returns

• plots : 2D and 3D embedding plots of subset

set_collection¶

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set_collection(
   collection = list(), file = 'Set_collection_', output_file = None,
   distance_matrix = None, metadata = None
)

Methods:

.calculate_distances¶

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.calculate_distances(
   method
)

Computes tree_set distance matrix with method of choice

Args

• method (str) : method/algorithm used to compute distance matrix

.concatenate¶

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.concatenate(
   other
)

Concatenates two collectionsor collection and tree_set

Args

• other (tree_set ot set_colletion) : tree_set ot set_colletion

Returns

• set_collection : concatenated set_collection