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Glossary

This tool may interest individuals with and without a background in computer science, so all users need to become familiar with the nomenclature used by LineageTree. To that end, this glossary defines the terms used throughout the project.

Tree Graphs

A tree graph is a hierarchical acyclic graph that contains nodes and edges, LineageTree is a tree graph that has at most 2 successors for one node. To create a demo tree the user can call

from lineagetree import LineageTree
lT = LineageTree(successors= {i:[i+1] for i in range(10)})

  • Nodes: The smallest part of a LineageTree, representing a point (usually a cell at a timepoint). All nodes can be accessed with lT.nodes.

  • Edges: Objects that connect two nodes. In a lineage tree the edges are directed. All edges can be accessed with lT.edges.

  • Successors: The successor of a node n at time t is the node n' at time t+1 that connects from n. The mapping of all successors can be accessed with lT.successor.

  • Predecessors: The predecessor of a node n at time t is the node n' at time t−1 that connects into n. The mapping of all predecessors can be accessed with lT.predecessor.

  • Roots: Nodes with no predecessors. In LineageTree, by deafualt, a root has an empty tuple as predecessor. Multiple roots may exist. All roots can be accessed with lT.roots.

  • Leaves: Nodes with no successors. In LineageTree, by deafualt, a leaf has an empty tuple as successor. All leaves can be accessed with lT.leaves.

  • Chains: A tree segment where all nodes lie between a root or division and a division or leaf. The chain containing node n can be accessed with lT.get_chain_of_node(n). A continuous part of a chain is a subchain or path.

  • Divisions: Events where one node has two successors instead of one. Divisions are inferred because the node before a division is at the end of a chain.

  • Subtree: Any tree segment that is itself a tree. The subtree rooted at a given node can be retrieved with lT.get_sub_tree(node).

  • Siblings: Two nodes that share the same predecessor. Often refers to the first nodes of chains originating from the same division.

  • Time: The discrete timepoint at which nodes exist (not real time). All node → time information can be accessed with lT.times.

  • Time resolution: The duration represented by one timepoint. Useful for comparing different lineages. This value can be accessed via lT.time_resolution.

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