skbio.stats.distance.SymmetricMatrix#

class skbio.stats.distance.SymmetricMatrix(data, ids=None, validate=True, condensed=False, diagonal=None)[source]#

Store symmetric pairwise relationships between objects.

A SymmetricMatrix is a PairwiseMatrix with the additional requirement that the matrix data is symmetric (i.e., upper and lower triangles mirror each other). There are additional methods made available that take advantage of this symmetry.

Added in version 0.7.1.

Parameters:

data1-D or 2-D array_like, or PairwiseMatrix: A square 2-D array of pairwise relationships between objects, or a 1-D array representing its condensed form. Can instead be an instance of PairwiseMatrix or its subclass, in which case its data and IDs will be directly used.
idssequence of str, optional: IDs of the objects. Must match the number of objects in data. If None (default) and data does not contain IDs, IDs will be monotonically-increasing integers cast as strings, starting from zero (i.e., ‘0’, ‘1’, ‘2’, ‘3’, …).
validatebool, optional: If True (default) and data is not a SymmetricMatrix object, the input data will be validated.
condensedbool, optional: Store the data in a 2-D redundant form (False, default) or a 1-D condensed form (True).
diagonal1-D array_like or float, optional: Values along the diagonal of the matrix. Can be a vector matching the number of objects in data, or a single number representing a uniform diagonal. Default is zero. Can be provided when data is in condensed form. Otherwise, an error will be raised.

See also

PairwiseMatrix
SymmetricMatrix
scipy.spatial.distance.squareform

Attributes

`T`	Transpose of the matrix.
`diagonal`	Diagonal value(s) of the matrix.

Attributes (inherited)

`data`	Array of pairwise relationships.
`default_write_format`
`dtype`	Data type of the matrix values.
`ids`	Tuple of object IDs.
`shape`	Two-element tuple containing the redundant form matrix dimensions.
`size`	Total number of elements in the underlying data structure.

Methods

`as_condensed`()	Return a condensed form deep copy of the matrix.
`as_redundant`()	Return a redundant form deep copy of the matrix.
`condensed_form`()	Return an array of distances in condensed format.
`copy`()	Return a deep copy of the symmetric matrix.
`from_iterable`(iterable, metric[, key, keys, ...])	Create a symmetric matrix from an iterable given a metric.
`permute`([condensed, seed])	Randomly permute both rows and columns in the matrix.
`redundant_form`()	Return an array of values in redundant format.
`transpose`()	Return the transpose of the matrix.

Methods (inherited)

`between`(from_, to_[, allow_overlap])	Obtain the pairwise values between the two groups of IDs.
`filter`(ids[, strict])	Filter the matrix by IDs.
`index`(lookup_id)	Return the index of the specified ID.
`plot`([cmap, title])	Create a heatmap of the matrix.
`read`([format])	Create a new `SymmetricMatrix` instance from a file.
`rename`(mapper[, strict])	Rename IDs in the matrix.
`to_data_frame`()	Create a pandas DataFrame from this matrix.
`within`(ids)	Obtain all the pairwise values among the set of IDs.
`write`(file[, format])	Write an instance of `SymmetricMatrix` to a file.

Special methods

__getitem__(index)

Slice into data by object ID or NumPy indexing.

Special methods (inherited)

`__contains__`(lookup_id)	Check if the specified ID is in the matrix.
`__eq__`(other)	Compare this matrix to another for equality.
`__ge__`(value, /)	Return self>=value.
`__getstate__`(/)	Helper for pickle.
`__gt__`(value, /)	Return self>value.
`__le__`(value, /)	Return self<=value.
`__lt__`(value, /)	Return self<value.
`__ne__`(other)	Determine whether two matrices are not equal.
`__str__`()	Return a string representation of the matrix.

Details

T#

Transpose of the matrix.

If the matrix is in condensed form, a redundant form matrix will be returned.