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As a result of pseudotime calculation, three types of cell nodes will become apparent on the plot (in addition to the intermediate nodes from the previous step).
- 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 in Figure xxx).
- 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 in Figure xxx).
- Leaf (light gray). Leaves correspond to different cell fates / different trajectory outcomes (e.g. nodes 3, 8, and 11 in Figure xxx). The leaves correspond to cell states of Monocle 2.
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