lineage.CellVar

This file contains the class for CellVar which holds the state and observation information in the hidden and observed trees respectively.

Classes

`Time`	Class that stores all the time related observations in a neater format.
`CellVar`	Cell class.

Module Contents

class lineage.CellVar.Time

Class that stores all the time related observations in a neater format. This assists in pruning based on experimental time and obtaining attributes of the lineage as a whole like the average growth rate.

startT: float

endT: float

transition_time: float = 0.0

class lineage.CellVar.CellVar(parent=None, state=-1)

Cell class.

Parameters:

parent (CellVar | None)
state (int)

parent: CellVar | None

gen: int

observed: bool

state: int

obs: numpy.ndarray | list[Any]

time: Time | None

left: CellVar | None

right: CellVar | None

divide(T, rng=None)

Member function that performs division of a cell. Equivalent to adding another timestep in a Markov process. :param T: The array containing the likelihood of a cell switching states.

Parameters:: T (numpy.ndarray)

isLeafBecauseTerminal()

Returns true when a cell is a leaf with no children. These are cells at the end of the tree.

Return type:: bool

isLeaf()

Returns true when a cell is a leaf defined by the two conditions that determine whether a cell is a leaf. A cell only has to satisfy one of the conditions (an or statement) for it to be a leaf.

Return type:: bool