tree_metrics.py - Stanza Demo

High-level description

This file provides functions for calculating tree metrics, specifically parsimony and likelihood, for a given CassiopeiaTree. It includes functions for calculating the number of mutations on a tree, the log likelihood of a character on a tree, and wrapper functions for calculating the overall likelihood of a tree under both discrete and continuous models of lineage tracing.

References

This code references the CassiopeiaTree class from cassiopeia.data and the parameter_estimators module from cassiopeia.tools.

Symbols

`calculate_parsimony`

Description

Calculates the parsimony score of a tree, defined as the number of character/state mutations that occur on the edges of the tree.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree to calculate parsimony over
infer_ancestral_characters	bool	Whether to infer the ancestral character states of the tree using Camin-Sokal Parsimony. Defaults to False.
treat_missing_as_mutation	bool	Whether to treat transitions from a non-missing state to a missing state as mutations. Defaults to False.

Outputs

Name	Type	Description
parsimony	int	The number of mutations that have occurred on the tree

Internal Logic

If infer_ancestral_characters is True, the ancestral character states of the tree are inferred using Camin-Sokal Parsimony.
The function iterates over all edges in the tree.
For each edge, it retrieves the character states of the parent and child nodes.
It then calculates the number of mutations along the edge using the get_mutations_along_edge method of the CassiopeiaTree object.
The total number of mutations is summed over all edges and returned.

`log_transition_probability`

Description

Calculates the log transition probability between two given states for a specific character.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree on which the priors are stored
character	int	The index of the character
s	Union[int, str]	The original state
s_	Union[int, str]	The state being transitioned to
t	float	The length of time that the transition can occur along
mutation_probability_function_of_time	Callable[[float], float]	The function defining the probability of a lineage acquiring a mutation within a given time
missing_probability_function_of_time	Callable[[float], float]	The function defining the probability of a lineage acquiring heritable missing data within a given time

Outputs

Name	Type	Description
log_probability	float	The log transition probability between the states

Internal Logic

The function calculates the log transition probability based on the following assumptions:

State 0 represents the uncut state.
Only state 0 can transition to non-zero states.
Any non-missing state can mutate to the missing state, specified by tree.missing_state_indicator.
The probability of acquiring a mutation is given by the time t and the mutation_probability_function_of_time.
The probability of acquiring heritable missing data is given by the time t and the missing_probability_function_of_time.
The priors on the tree (tree.priors) are used to determine the probability of acquiring a non-missing, non-zero state.

The function uses a series of conditional statements to handle different combinations of s and s_ and returns the corresponding log transition probability.

`log_likelihood_of_character`

Description

Calculates the log likelihood of a given character on the tree using Felsenstein’s Pruning Algorithm.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree on which to calculate the likelihood
character	int	The index of the character to calculate the likelihood of
use_internal_character_states	bool	Indicates if internal node character states should be assumed to be specified exactly. Defaults to False.
mutation_probability_function_of_time	Callable[[float], float]	The function defining the probability of a lineage acquiring a mutation within a given time
missing_probability_function_of_time	Callable[[float], float]	The function defining the probability of a lineage acquiring heritable missing data within a given time
stochastic_missing_probability	float	The probability that a cell/character pair acquires stochastic missing data at the end of the lineage
implicit_root_branch_length	float	The length of the implicit root branch. Used if the implicit root needs to be added. Defaults to 1.

Outputs

Name	Type	Description
log_likelihood	float	The log likelihood of the tree on one character

Internal Logic

The function performs a depth-first traversal of the tree in postorder.
For each node, it calculates the likelihood of each possible state at that node based on the likelihoods of its children and the transition probabilities between states.
If use_internal_character_states is False, the function assumes an implicit root with the uncut state (0) at each character and marginalizes over the transition from the implicit root to its child.
If use_internal_character_states is True, the function returns the likelihood of the state annotated at the root for the given character.

`get_lineage_tracing_parameters`

Description

Retrieves or estimates the lineage tracing parameters (mutation rate, heritable missing rate, and stochastic missing probability) from a CassiopeiaTree.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree from which to retrieve or estimate the parameters
continuous	bool	If the parameters are to be estimated, whether to estimate them as continuous or discrete parameters
assume_root_implicit_branch	bool	In the tree depth/time in estimating the rate parameters, whether or not to include an implicit root
layer	Optional[str]	Layer to use for the character matrix in estimating parameters. If None, the current `character_matrix` variable will be used. Defaults to None.

Outputs

Name	Type	Description
mutation_rate	float	The mutation rate
heritable_missing_rate	float	The heritable missing rate
stochastic_missing_probability	float	The stochastic missing probability

Internal Logic

The function attempts to retrieve the parameters from tree.parameters.
If any of the parameters are not found, they are estimated using the estimate_mutation_rate and estimate_missing_data_rates functions.
The function checks if the estimated parameters have valid values and raises a TreeMetricError if they are invalid.

`calculate_likelihood_discrete`

Description

Calculates the log likelihood of a tree under a discrete model of lineage tracing.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree on which to calculate likelihood over
use_internal_character_states	bool	Indicates if internal node character states should be assumed to be specified exactly. Defaults to False.
layer	Optional[str]	Layer to use for the character matrix in estimating parameters. If None, the current `character_matrix` variable will be used. Defaults to None.

Outputs

Name	Type	Description
log_likelihood	float	The log likelihood of the tree given the observed character states

Internal Logic

The function retrieves the lineage tracing parameters using get_lineage_tracing_parameters.
It calculates the log likelihood for each character using log_likelihood_of_character with discrete rate functions.
The log likelihoods of all characters are summed to obtain the overall log likelihood of the tree.

`calculate_likelihood_continuous`

Description

Calculates the log likelihood of a tree under a continuous model of lineage tracing.

Inputs

Name	Type	Description
tree	CassiopeiaTree	The tree on which to calculate likelihood over
use_internal_character_states	bool	Indicates if internal node character states should be assumed to be specified exactly. Defaults to False.
layer	Optional[str]	Layer to use for the character matrix in estimating parameters. If None, the current `character_matrix` variable will be used. Defaults to None.

Outputs

Name	Type	Description
log_likelihood	float	The log likelihood of the tree given the observed character states

Internal Logic

The function retrieves the lineage tracing parameters using get_lineage_tracing_parameters.
It calculates the log likelihood for each character using log_likelihood_of_character with continuous rate functions.
The log likelihoods of all characters are summed to obtain the overall log likelihood of the tree.

Error Handling

The functions in this file raise TreeMetricError exceptions if the input tree is not initialized or if the character states are not properly initialized. They also raise TreeMetricError exceptions if the lineage tracing parameters have invalid values.

​High-level description

​References

​Symbols

​calculate_parsimony

​Description

​Inputs

​Outputs

​Internal Logic

​log_transition_probability

​Description

​Inputs

​Outputs

​Internal Logic

​log_likelihood_of_character

​Description

​Inputs

​Outputs

​Internal Logic

​get_lineage_tracing_parameters

​Description

​Inputs

​Outputs

​Internal Logic

​calculate_likelihood_discrete

​Description

​Inputs

​Outputs

​Internal Logic

​calculate_likelihood_continuous

​Description

​Inputs

​Outputs

​Internal Logic

​Error Handling

High-level description

References

Symbols

`calculate_parsimony`

Description

Inputs

Outputs

Internal Logic

`log_transition_probability`

Description

Inputs

Outputs

Internal Logic

`log_likelihood_of_character`

Description

Inputs

Outputs

Internal Logic

`get_lineage_tracing_parameters`

Description

Inputs

Outputs

Internal Logic

`calculate_likelihood_discrete`

Description

Inputs

Outputs

Internal Logic

`calculate_likelihood_continuous`

Description

Inputs

Outputs

Internal Logic

Error Handling