Continuous structure in the data: PAGA topology between clusters, diffusion map and DPT pseudotime, a force-directed layout, and RNA velocity from spliced / unspliced counts (scvelo stochastic or dynamical mode) with its velocity graph, latent time and terminal states.
Typical pipelines
Pseudotime: Neighbors → Diffusion Map → DPT (with PAGA alongside) → Trajectory Visualization. Velocity: a loader that keeps spliced / unspliced layers → RNA Velocity → Velocity Graph → Velocity Visualization, and in dynamical mode → Latent Time → Terminal States.
Draw Graph uses ForceAtlas2 when it is available and otherwise falls back to Fruchterman–Reingold. Since v0.25.0 the node reports the layout it actually used (in the stored obsm key and in the Methods text) and the layout is seeded, so the same seed gives the same picture.
Common pitfalls
DPT needs a root. Pick the root cell or root cluster deliberately; pseudotime is 0 at the root and grows away from it.
Velocity needs velocity layers. A plain H5AD without spliced / unspliced layers cannot run RNA Velocity — use Load Velocyto Loom, Load STARsolo Velocity, or an H5AD that already carries them.
Latent Time is dynamical-mode only. Stochastic velocity does not fit the kinetics Latent Time is derived from.
Partition-based Graph Abstraction — coarse-grained trajectory topology between clusters.
| Name | Type | Default | Description |
|---|---|---|---|
groups | obs column | leiden | Cluster column. |
model | select | v1.2 | "v1.2" (improved) or "v1.0". |
use_rna_velocity | checkbox | false | Directed edges from RNA velocity. |
Diffusion Pseudotime — orders cells along a continuous trajectory (0 = root, 1 = differentiated).
| Name | Type | Default | Description |
|---|---|---|---|
groups | obs column | leiden | Cluster column. |
n_dcs | number | 10 | Diffusion components. |
root_group | text | — | Root cluster name. |
root_cell | number | — | Index of root cell (overrides root_group). |
n_branchings | number | 0 | Number of branchings to detect. |
min_group_size | number | 0.01 | Minimum fraction of cells per group. |
Diffusion map embedding — captures continuous transitions. Required before DPT.
| Name | Type | Default | Description |
|---|---|---|---|
n_comps | number | 15 | Number of diffusion components. |
Force-directed graph layout (ForceAtlas2 / Fruchterman-Reingold).
| Name | Type | Default | Description |
|---|---|---|---|
layout | select | fa | fa/fr/drl/kk. |
init_pos | select | paga | paga (recommended)/spectral/random. |
n_iterations | number | — | Number of iterations. null = auto. |
random_state | number | 0 | Random seed. |
Estimate RNA velocity from spliced/unspliced counts (scvelo).
| Name | Type | Default | Description |
|---|---|---|---|
mode | select | stochastic | stochastic/deterministic/dynamical. |
n_top_genes | number | 2000 | Top variable genes for velocity. |
min_shared_counts | number | 20 | Min shared spliced/unspliced. |
n_neighbors | number | 30 | Neighbors for moment computation. |
n_pcs | number | 30 | PCA components. |
enforce | checkbox | false | Force recomputation even if results exist. |
Compute velocity transition graph for stream/arrow plots.
| Name | Type | Default | Description |
|---|---|---|---|
n_neighbors | number | — | Neighbors for graph. |
approx | checkbox | false | Approximate the velocity graph on a PCA subspace. Off (exact, the scVelo default) is recommended; on is faster but can flip arrow directions. |
n_recurse_neighbors | number | — | Number of recursive neighbors. null = auto. |
Latent time from dynamical RNA velocity. More accurate than DPT when velocity available.
| Name | Type | Default | Description |
|---|---|---|---|
min_likelihood | number | 0.1 | Gene likelihood threshold. |
root_key | text | — | Root cells key (auto-detect if empty). |
end_key | text | — | Key for terminal cells. Empty = auto-detect. |
Identify terminal/initial states from velocity transition matrix.
| Name | Type | Default | Description |
|---|---|---|---|
groupby | obs column | — | Cluster column for grouping. |
self_transitions | checkbox | false | Include self-transitions. |
