bio-single-cell-trajectory-inference

Monocle3 (R)

Goal: Infer developmental trajectories and pseudotime ordering using Monocle3's principal graph approach.

Approach: Learn a principal graph through the data manifold, order cells along the graph from a root state, and extract pseudotime values.

"Find the developmental trajectory in my data" → Construct a tree-like graph through the cell embedding, assign pseudotime from a root population, and identify branch points.

library(monocle3)

## Order cells (select root interactively or programmatically)

cds <- order_cells(cds, root_cells = root_cell_ids)

## Plot trajectory with pseudotime

plot_cells(cds, color_cells_by = 'pseudotime', label_branch_points = TRUE, label_leaves = TRUE)