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1. Root node (white). Root nodes are start points of the pseudotime and were defined by the user in the previous step (e.g. node 7 4 in Figure 6).
2. Branch node (black). Branch nodes indicate where the trajectory tree forks out; i.e. each branch represents a different cell fate or different trajectory (e.g. nodes 1 and 4 3-6, and 8 in Figure 6).
3. Leaf (light gray). Leaves correspond to different cell fates / different trajectory outcomes (e.g. nodes 35, 89, and 11 12 in Figure 6). The leaves correspond to cell states of Monocle 2.

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Automatic Selection of the Root Node

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