def setup_root_finder(self, cassiopeia_tree: CassiopeiaTree) -> None:
"""Gives the implicit rooting strategy for the SNJ Solver.
By default, the SpectralNeighborJoining algorithm returns an
unrooted tree. To root this tree, an implicit root of all zeros is
added to the character matrix. Then, the dissimilarity map is
recalculated using the updated character matrix. If the tree already
has a computed dissimilarity map, only the new similarities are
calculated. See 'setup_root_finder' in NeighborJoiningSolver.
Args:
cassiopeia_tree: Input CassiopeiaTree to `solve`
"""
character_matrix = cassiopeia_tree.character_matrix.copy()
rooted_character_matrix = character_matrix.copy()
root = [0] * rooted_character_matrix.shape[1]
rooted_character_matrix.loc["root"] = root
cassiopeia_tree.root_sample_name = "root"
cassiopeia_tree.character_matrix = rooted_character_matrix
if self.dissimilarity_function is None:
raise DistanceSolver.DistanceSolverError(
"Please specify a dissimilarity function to add an implicit "
"root, or specify an explicit root"
)
dissimilarity_map = cassiopeia_tree.get_dissimilarity_map()
if dissimilarity_map is None:
cassiopeia_tree.compute_dissimilarity_map(
self.dissimilarity_function, self.prior_transformation
)
else:
dissimilarity = {"root": 0}
for leaf in character_matrix.index:
weights = None
if cassiopeia_tree.priors:
weights = solver_utilities.transform_priors(
cassiopeia_tree.priors, self.prior_transformation
)
dissimilarity[leaf] = self.dissimilarity_function(
rooted_character_matrix.loc["root"].values,
rooted_character_matrix.loc[leaf].values,
cassiopeia_tree.missing_state_indicator,
weights,
)
cassiopeia_tree.set_dissimilarity("root", dissimilarity)
cassiopeia_tree.character_matrix = character_matrix
def setup_dissimilarity_map(self,
cassiopeia_tree: CassiopeiaTree,
layer: Optional[str] = None) -> None:
"""Sets up the solver.
Sets up the solver with respect to the input CassiopeiaTree by
creating the dissimilarity map if needed and setting up the
"root" sample if the tree will be rooted. Operates directly on the
CassiopeiaTree.
Args:
cassiopeia_tree: Input CassiopeiaTree to `solve`.
layer: Layer storing the character matrix for solving. If None, the
default character matrix is used in the CassiopeiaTree.
Raises:
A `DistanceSolverError` if rooting parameters are not passed in
correctly (i.e. no root is specified and the user has not
asked to find a root) or when a dissimilarity map cannot
be found or computed.
"""
# if root sample is not specified, we'll add the implicit root
# and recompute the dissimilarity map
if cassiopeia_tree.root_sample_name is None:
if self.add_root:
self.setup_root_finder(cassiopeia_tree)
else:
raise DistanceSolverError(
"Please specify an explicit root sample in the Cassiopeia Tree"
" or specify the solver to add an implicit root")
if cassiopeia_tree.get_dissimilarity_map() is None:
if self.dissimilarity_function is None:
raise DistanceSolverError(
"Please specify a dissimilarity function or populate the "
"CassiopeiaTree object with a dissimilarity map")
cassiopeia_tree.compute_dissimilarity_map(
self.dissimilarity_function, self.prior_transformation, layer)
def compute_cophenetic_correlation(
tree: CassiopeiaTree,
weights: Optional[pd.DataFrame] = None,
dissimilarity_map: Optional[pd.DataFrame] = None,
dissimilarity_function: Optional[
Callable[[np.array, np.array, int, Dict[int, Dict[int, float]]], float]
] = dissimilarity_functions.weighted_hamming_distance,
) -> Tuple[float, float]:
"""Computes the cophenetic correlation of a lineage.
Computes the cophenetic correlation of a lineage, which is defined as the
Pearson correlation between the phylogenetic distance and dissimilarity
between characters.
If neither weight matrix nor the dissimilarity map are precomputed, then
this function will run in O(mn^2 + n^2logn + n^2) time, as the dissimilarity
map will take O(mn^2) time, the phylogenetic distance will take O(n^2 logn)
time, and the Pearson correlation will take O(n^2) time since it must
compare n^2 entries (n = number of leaves; m = number of characters).
Args:
tree: CassiopeiaTree
weights: Phylogenetic weights matrix. If this is not specified, invokes
`cas.data.compute_phylogenetic_weight_matrix`
dissimilarity_map: Dissimilarity matrix between samples. If this is not
specified, then `tree.compute_dissimilarity_map` will be called.
dissimilarity_function: Dissimilarity function to use. If dissimilarity
map is not passed in, and one does not already exist in the
CassiopeiaTree, then this function will be used to compute the
dissimilarities between samples.
Returns:
The cophenetic correlation value and significance for the tree.
"""
# set phylogenetic weight matrix
W = (
compute_phylogenetic_weight_matrix(tree)
if (weights is None)
else weights
)
# set dissimilarity map
D = (
tree.get_dissimilarity_map()
if (dissimilarity_map is None)
else dissimilarity_map
)
if D is None:
tree.compute_dissimilarity_map(
dissimilarity_function=dissimilarity_function
)
D = tree.get_dissimilarity_map()
# align matrices
cells = tree.leaves
W = W.loc[cells, cells]
D = D.loc[cells, cells]
# convert to condensed distance matrices
Wp = spatial.distance.squareform(W)
Dp = spatial.distance.squareform(D)
return stats.pearsonr(Wp, Dp)