DenseTaxaMatrix

class pybrops.core.mat.DenseTaxaMatrix.DenseTaxaMatrix(mat, taxa=None, taxa_grp=None, **kwargs)

Bases: DenseMutableMatrix, TaxaMatrix

A concrete class for dense matrices with taxa metadata.

The purpose of this concrete class is to implement base functionality for:

1. Dense matrix taxa metadata.

2. Dense matrix taxa routines.

Constructor for the concrete class DenseTaxaMatrix.

Parameters:

• mat (numpy.ndarray) – A numpy.ndarray used to construct the object.

• taxa (numpy.ndarray, None) – A numpy.ndarray of shape (n,) containing taxa names. If None, do not store any taxa name information.

• taxa_grp (numpy.ndarray, None) – A numpy.ndarray of shape (n,) containing taxa groupings. If None, do not store any taxa group information.

• kwargs (dict) – Additional keyword arguments.

Methods

adjoin	Add additional elements to the end of the Matrix along an axis.
adjoin_taxa	Add additional elements to the end of the TaxaMatrix along the taxa axis.
append	Append values to the matrix.
append_taxa	Append values to the Matrix along the taxa axis.
concat	Concatenate matrices together along an axis.
concat_taxa	Concatenate list of Matrix together along the taxa axis.
copy	Make a shallow copy of the Matrix.
deepcopy	Make a deep copy of the Matrix.
delete	Delete sub-arrays along an axis.
delete_taxa	Delete sub-arrays along the taxa axis.
from_hdf5	Read DenseTaxaMatrix from an HDF5 file.
group	Sort the DenseTaxaMatrix along an axis, then populate grouping indices.
group_taxa	Sort the Matrix along the taxa axis, then populate grouping indices for the taxa axis.
incorp	Incorporate values along the given axis before the given indices.
incorp_taxa	Incorporate values along the taxa axis before the given indices.
insert	Insert values along the given axis before the given indices.
insert_taxa	Insert values along the taxa axis before the given indices.
is_grouped	Determine whether the Matrix has been sorted and grouped.
is_grouped_taxa	Determine whether the Matrix has been sorted and grouped along the taxa axis.
lexsort	Perform an indirect stable sort using a tuple of keys.
lexsort_taxa	Perform an indirect stable sort using a sequence of keys along the taxa axis.
remove	Remove sub-arrays along an axis.
remove_taxa	Remove sub-arrays along the taxa axis.
reorder	Reorder values in the DenseTaxaMatrix.
reorder_taxa	Reorder elements of the Matrix along the taxa axis using an array of indices.
select	Select certain values from the matrix.
select_taxa	Select certain values from the Matrix along the taxa axis.
sort	Reset metadata for corresponding axis: name, stix, spix, len.
sort_taxa	Sort slements of the Matrix along the taxa axis using a sequence of keys.
to_hdf5	Write DenseTaxaMatrix to an HDF5 file.
ungroup	Ungroup the DenseTaxaMatrix along an axis by removing grouping metadata.
ungroup_taxa	Ungroup the DenseTaxaMatrix along the taxa axis by removing taxa group metadata.

Attributes

mat	Pointer to raw numpy.ndarray object.
mat_ndim	Number of dimensions of the raw numpy.ndarray.
mat_shape	Shape of the raw numpy.ndarray.
ntaxa	Number of taxa
taxa	Taxa label array
taxa_axis	Axis along which taxa are stored
taxa_grp	Taxa group label.
taxa_grp_len	Taxa group length.
taxa_grp_name	Taxa group name.
taxa_grp_spix	Taxa group stop index.
taxa_grp_stix	Taxa group start index.

__add__(value)

Elementwise add matrices

Parameters:

value (object) – Object which to add.

Returns:

out – An object resulting from the addition.

Return type:

object

__mul__(value)

Elementwise multiply matrices

Parameters:

value (object) – Object which to multiply.

Returns:

out – An object resulting from the multiplication.

Return type:

object

adjoin(values, axis=-1, taxa=None, taxa_grp=None, **kwargs)

Add additional elements to the end of the Matrix along an axis.

Parameters:

• values (DensePhasedGenotypeMatrix, numpy.ndarray) – Values to be appended to append to the Matrix.

• axis (int) – The axis along which values are adjoined.

• taxa (numpy.ndarray) – Taxa names to adjoin to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa field, providing this argument overwrites the field.

• taxa_grp (numpy.ndarray) – Taxa groups to adjoin to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa_grp field, providing this argument overwrites the field.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of mat with values appended to axis. Note that adjoin does not occur in-place: a new Matrix is allocated and filled.

Return type:

DenseTaxaMatrix

adjoin_taxa(values, taxa=None, taxa_grp=None, **kwargs)

Add additional elements to the end of the TaxaMatrix along the taxa axis. Copy-on-manipulation routine.

Parameters:

• values (DensePhasedGenotypeMatrix, numpy.ndarray) – Values to be appended to append to the Matrix.

• taxa (numpy.ndarray) – Taxa names to adjoin to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa field, providing this argument overwrites the field.

• taxa_grp (numpy.ndarray) – Taxa groups to adjoin to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa_grp field, providing this argument overwrites the field.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A copy of the TaxaMatrix with values appended to the taxa axis Note that adjoin does not occur in-place: a new Matrix is allocated and filled.

Return type:

DenseTaxaMatrix

append(values, axis=-1, taxa=None, taxa_grp=None, **kwargs)

Append values to the matrix.

Parameters:

• values (DenseTaxaMatrix, numpy.ndarray) – Values are appended to append to the matrix. Must be of type int8. Must be of shape (m, n, p)

• axis (int) – The axis along which values are appended.

• taxa (numpy.ndarray) – Taxa names to append to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa field, providing this argument overwrites the field.

• taxa_grp (numpy.ndarray) – Taxa groups to append to the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa_grp field, providing this argument overwrites the field.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

append_taxa(values, taxa=None, taxa_grp=None, **kwargs)

Append values to the Matrix along the taxa axis.

Parameters:

• values (Matrix, numpy.ndarray) – Values are appended to append to the matrix.

• taxa (numpy.ndarray) – Taxa names to append to the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to append to the Matrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

classmethod concat(mats, axis=-1, **kwargs)

Concatenate matrices together along an axis.

Parameters:

• mats (Sequence of matrices) – List of Matrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.

• axis (int) – The axis along which the arrays will be joined.

• kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated DenseTaxaMatrix. Note that concat does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

classmethod concat_taxa(mats, **kwargs)

Concatenate list of Matrix together along the taxa axis.

Parameters:

• mats (Sequence of Matrix) – List of Matrix to concatenate. The matrices must have the same shape, except in the dimension corresponding to axis.

• kwargs (dict) – Additional keyword arguments

Returns:

out – The concatenated DenseTaxaMatrix. Note that concat does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

copy()

Make a shallow copy of the Matrix.

Returns:

out – A shallow copy of the original DenseMatrix.

Return type:

DenseMatrix

deepcopy(memo=None)

Make a deep copy of the Matrix.

Parameters:

memo (dict) – Dictionary of memo metadata.

Returns:

out – A deep copy of the original DenseMatrix.

Return type:

DenseMatrix

delete(obj, axis=-1, **kwargs)

Delete sub-arrays along an axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• axis (int) – The axis along which to delete the subarray defined by obj.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A DenseTaxaMatrix with deleted elements. Note that concat does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

delete_taxa(obj, **kwargs)

Delete sub-arrays along the taxa axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A DenseTaxaMatrix with deleted elements. Note that concat does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

classmethod from_hdf5(filename, groupname=None)

Read DenseTaxaMatrix from an HDF5 file.

Parameters:

• filename (str, Path, h5py.File) – If str or Path, an HDF5 file name from which to read. File is closed after reading. If h5py.File, an opened HDF5 file from which to read. File is not closed after reading.

• groupname (str, None) – If str, an HDF5 group name under which DenseTaxaMatrix data is stored. If None, DenseTaxaMatrix is read from base HDF5 group.

Returns:

out – A dense matrix read from file.

Return type:

DenseTaxaMatrix

group(axis=-1, **kwargs)

Sort the DenseTaxaMatrix along an axis, then populate grouping indices.

Parameters:

• axis (int) – The axis along which values are grouped.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

group_taxa(**kwargs)

Sort the Matrix along the taxa axis, then populate grouping indices for the taxa axis.

Parameters:

kwargs (dict) – Additional keyword arguments.

Return type:

None

incorp(obj, values, axis=-1, taxa=None, taxa_grp=None, **kwargs)

Incorporate values along the given axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.

• values (array_like) – Values to incorporate into the matrix.

• axis (int) – The axis along which values are incorporated.

• taxa (numpy.ndarray) – Taxa names to incorporate into the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa field, providing this argument overwrites the field.

• taxa_grp (numpy.ndarray) – Taxa groups to incorporate into the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa_grp field, providing this argument overwrites the field.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

incorp_taxa(obj, values, taxa=None, taxa_grp=None, **kwargs)

Incorporate values along the taxa axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is incorporated.

• values (Matrix, numpy.ndarray) – Values to incorporate into the matrix.

• taxa (numpy.ndarray) – Taxa names to incorporate into the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to incorporate into the Matrix.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

insert(obj, values, axis=-1, taxa=None, taxa_grp=None, **kwargs)

Insert values along the given axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.

• values (Matrix, numpy.ndarray) – Values to insert into the matrix.

• axis (int) – The axis along which values are inserted.

• taxa (numpy.ndarray) – Taxa names to insert into the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa field, providing this argument overwrites the field.

• taxa_grp (numpy.ndarray) – Taxa groups to insert into the Matrix. If values is a DenseTaxaMatrix that has a non-None taxa_grp field, providing this argument overwrites the field.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A DenseTaxaMatrix with values inserted. Note that insert does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

insert_taxa(obj, values, taxa=None, taxa_grp=None, **kwargs)

Insert values along the taxa axis before the given indices.

Parameters:

• obj (int, slice, or Sequence of ints) – Object that defines the index or indices before which values is inserted.

• values (Matrix, numpy.ndarray) – Values to insert into the matrix.

• taxa (numpy.ndarray) – Taxa names to insert into the Matrix.

• taxa_grp (numpy.ndarray) – Taxa groups to insert into the Matrix.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – A DenseTaxaMatrix with values inserted. Note that insert does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

is_grouped(axis=-1, **kwargs)

Determine whether the Matrix has been sorted and grouped.

Parameters:

• axis (int) – The axis along which to test if values are grouped.

• kwargs (dict) – Additional keyword arguments.

Returns:

grouped – True or False indicating whether the GeneticMap has been sorted and grouped.

Return type:

bool

is_grouped_taxa(**kwargs)

Determine whether the Matrix has been sorted and grouped along the taxa axis.

Parameters:

kwargs (dict) – Additional keyword arguments.

Returns:

grouped – True or False indicating whether the Matrix has been sorted and grouped.

Return type:

bool

lexsort(keys, axis=-1, **kwargs)

Perform an indirect stable sort using a tuple of keys.

Parameters:

• keys (tuple, None) – A tuple of columns to be sorted. The last column is the primary sort key.

• axis (int) – The axis of the Matrix over which to sort values.

• kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys.

Return type:

numpy.ndarray

lexsort_taxa(keys=None, **kwargs)

Perform an indirect stable sort using a sequence of keys along the taxa axis.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Returns:

indices – Array of indices that sort the keys along the specified axis.

Return type:

A (N,) ndarray of ints

property mat: ndarray

Pointer to raw numpy.ndarray object.

property mat_ndim: int

Number of dimensions of the raw numpy.ndarray.

property mat_shape: tuple

Shape of the raw numpy.ndarray.

property ntaxa: int

Number of taxa

remove(obj, axis=-1, **kwargs)

Remove sub-arrays along an axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• axis (int) – The axis along which to remove the subarray defined by obj.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

remove_taxa(obj, **kwargs)

Remove sub-arrays along the taxa axis.

Parameters:

• obj (int, slice, or Sequence of ints) – Indicate indices of sub-arrays to remove along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

reorder(indices, axis=-1, **kwargs)

Reorder values in the DenseTaxaMatrix.

Parameters:

• indices (numpy.ndarray) – Indices of where to place elements.

• axis (int) – The axis over which to reorder values.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

reorder_taxa(indices, **kwargs)

Reorder elements of the Matrix along the taxa axis using an array of indices. Note this modifies the Matrix in-place.

Parameters:

• indices (A (N,) ndarray of ints) – Array of indices that reorder the matrix along the specified axis.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

select(indices, axis=-1, **kwargs)

Select certain values from the matrix.

Parameters:

• indices (array_like (Nj, ...)) – The indices of the values to select.

• axis (int) – The axis along which values are selected.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – The output DenseTaxaMatrix with values selected. Note that select does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

select_taxa(indices, **kwargs)

Select certain values from the Matrix along the taxa axis.

Parameters:

• indices (array_like (Nj, ...)) – The indices of the values to select.

• kwargs (dict) – Additional keyword arguments.

Returns:

out – The output DenseTaxaMatrix with values selected. Note that select does not occur in-place: a new DenseTaxaMatrix is allocated and filled.

Return type:

DenseTaxaMatrix

sort(keys, axis=-1, **kwargs)

Reset metadata for corresponding axis: name, stix, spix, len. Sort the VariantMatrix using a tuple of keys.

Parameters:

• keys (tuple, None) – A tuple of columns to be sorted. The last column is the primary sort key.

• axis (int) – The axis over which to sort values.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

sort_taxa(keys=None, **kwargs)

Sort slements of the Matrix along the taxa axis using a sequence of keys. Note this modifies the Matrix in-place.

Parameters:

• keys (A (k, N) array or tuple containing k (N,)-shaped sequences) – The k different columns to be sorted. The last column (or row if keys is a 2D array) is the primary sort key.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

property taxa: ndarray | None

Taxa label array

property taxa_axis: int

Axis along which taxa are stored

property taxa_grp: ndarray | None

Taxa group label.

property taxa_grp_len: ndarray | None

Taxa group length.

property taxa_grp_name: ndarray | None

Taxa group name.

property taxa_grp_spix: ndarray | None

Taxa group stop index.

property taxa_grp_stix: ndarray | None

Taxa group start index.

to_hdf5(filename, groupname=None, overwrite=True)

Write DenseTaxaMatrix to an HDF5 file.

Parameters:

• filename (str, Path, h5py.File) – If str, an HDF5 file name to which to write. File is closed after writing. If h5py.File, an opened HDF5 file to which to write. File is not closed after writing.

• groupname (str, None) – If str, an HDF5 group name under which the DenseTaxaMatrix data is stored. If None, the DenseTaxaMatrix is written to the base HDF5 group.

• overwrite (bool) – Whether to overwrite values in an HDF5 file if a field already exists.

Return type:

None

ungroup(axis=-1, **kwargs)

Ungroup the DenseTaxaMatrix along an axis by removing grouping metadata.

Parameters:

• axis (int) – The axis along which values should be ungrouped.

• kwargs (dict) – Additional keyword arguments.

Return type:

None

ungroup_taxa(**kwargs)

Ungroup the DenseTaxaMatrix along the taxa axis by removing taxa group metadata.

Parameters:

kwargs (dict) – Additional keyword arguments.

Return type:

None