omicverse-single-cell-sctour-trajectory

name	omicverse-single-cell-sctour-trajectory
description	Run the OmicVerse sctour trajectory branch on raw-count single-cell AnnData. Use when adapting the scTour part of an OmicVerse trajectory notebook, or when you need sctour pseudotime, latent space, or vector-field outputs instead of the diffusion_map, slingshot, or palantir branches.

OmicVerse Single-Cell scTour Trajectory

Goal

Run the sctour branch of ov.single.TrajInfer on a raw-count AnnData and capture the trainer-produced pseudotime, latent space, and vector field. Keep this separate from the lighter graph-based trajectory skill because it has a different dependency and compute profile.

Quick Workflow

1. Inspect the input AnnData and confirm raw UMI counts are available in .X.
2. Preserve or restore counts into .X before the sctour call.
3. Instantiate ov.single.TrajInfer(...) with the plotting basis, groupby, and any existing representation you want to preserve for downstream plots.
4. Run TrajInfer.inference(method='sctour', **trainer_kwargs).
5. Validate that pseudotime, latent coordinates, and vector-field outputs were written.
6. For lineage topology, draw the unified trajectory backbone with ov.pl.trajectory(adata, method='sctour', ...) or overlay on a custom UMAP with ov.pl.trajectory_overlay(adata, ax=ax, method='sctour') — same visual grammar shared with the other trajectory skills (commit 4f28ab6).
7. Summarize branch structure with ov.pl.branch_streamplot(adata, group_key=..., pseudotime_key='sctour_pseudotime').
8. Fit marker trends with the shared GAM stack: ov.single.dynamic_features(adata, genes=..., pseudotime='sctour_pseudotime') → ov.pl.dynamic_trends(...); many-gene panels via ov.pl.dynamic_heatmap(...).
9. Only invert or rescale pseudotime after fit when that direction change is biologically justified for the dataset.

Interface Summary

Fitting

• ov.single.TrajInfer(...) is still the public entrypoint.
• TrajInfer.inference(method='sctour', **kwargs) dispatches the sctour branch.
• In the current wrapper source, the branch internally calls sct.train.Trainer(self.adata, loss_mode='nb', **kwargs).
• The wrapper then calls tnode.train(), stores adata.obs['sctour_pseudotime'] = tnode.get_time(), stores adata.obsm['X_TNODE'] from tnode.get_latentsp(alpha_z=0.5, alpha_predz=0.5), and stores adata.obsm['X_VF'] from tnode.get_vector_field(...).

Visualisation (shared with other trajectory skills)

• ov.pl.trajectory(adata, method='sctour', basis='X_umap', color=...) — unified trajectory plot.
• ov.pl.trajectory_overlay(adata, ax=ax, method='sctour') — overlay backbone on existing embedding.
• ov.pl.branch_streamplot(adata, group_key=..., pseudotime_key='sctour_pseudotime', show=False) — river-style view.
• ov.single.dynamic_features(adata, genes=..., pseudotime='sctour_pseudotime', ...) + ov.pl.dynamic_trends(...) — per-gene GAM curves.
• ov.pl.dynamic_heatmap(adata, pseudotime='sctour_pseudotime', var_names=..., ...) — many-gene panel.

Read references/source-grounding.md before adding more interface-specific detail.

Boundary

• Keep sctour separate from the shared diffusion_map / slingshot / palantir skill.
• Do not fold preprocessing or clustering into this skill unless the real request is upstream data preparation; hand off to the preprocessing skill first.
• Do not use this skill when the user only wants DPT pseudotime, lineage curves, or Palantir fate probabilities; use the trajectory-inference skill instead.

Stage Selection

• Use this skill only when the requested branch is explicitly method='sctour' or when the user asks for scTour latent-space or vector-field outputs.
• Keep the notebook's alpha_recon_lec and alpha_recon_lode values as branch examples, not universal defaults.
• Treat the wrapper's fixed loss_mode='nb' as part of the current execution path; if a different loss mode is needed, inspect the underlying sctour package before changing the workflow.

Input Contract

• Start from AnnData.
• Ensure raw UMI counts are present in .X for the default negative-binomial loss path.
• Preserve a plotting basis such as X_umap only if you want to overlay sctour_pseudotime later.
• Preserve cluster annotations only if you need grouped plots or interpretation after training.

Minimal Execution Pattern

import omicverse as ov

traj = ov.single.TrajInfer(
    adata,
    basis="X_umap",
    use_rep="X_pca",
    groupby="clusters",
)
traj.inference(
    method="sctour",
    alpha_recon_lec=0.5,
    alpha_recon_lode=0.5,
)

# Optional notebook-specific direction flip only if biologically justified.
adata.obs["sctour_pseudotime"] = 1 - adata.obs["sctour_pseudotime"]

# Unified trajectory plots
ov.pl.trajectory(adata, method="sctour", basis="X_umap", color="clusters")

fig, ax = ov.plt.subplots(figsize=(4, 4))
ov.pl.embedding(adata, basis="X_umap", color="clusters", ax=ax, show=False)
ov.pl.trajectory_overlay(adata, ax=ax, method="sctour")

# Branch streamplot + marker dynamics on sctour_pseudotime
ov.pl.branch_streamplot(
    adata, group_key="clusters", pseudotime_key="sctour_pseudotime", show=False,
)
res = ov.single.dynamic_features(
    adata, genes=["Pdx1", "Ins1", "Gcg"],
    pseudotime="sctour_pseudotime", store_raw=True, raw_obs_keys=["clusters"],
)
ov.pl.dynamic_trends(res, genes=["Pdx1", "Ins1", "Gcg"],
                    add_point=True, point_color_by="clusters")

Constraints

• Keep raw counts in .X before training; the wrapper hardcodes loss_mode='nb'.
• Treat the notebook's pseudotime inversion as optional and dataset-specific.
• This branch depends on the external sctour package and was not fully executable in the current local environment.
• Do not promise GPU use or full-scale training unless the runtime and dependency stack are confirmed.

Validation

• Confirm adata.obs['sctour_pseudotime'] exists after the fit.
• Confirm adata.obsm['X_TNODE'] exists after the fit.
• Confirm adata.obsm['X_VF'] exists after the fit.
• If you invert pseudotime, record that postprocessing step explicitly.
• If the environment cannot import sctour, treat the branch as source-grounded but not empirically reproduced.

Resource Map

• Read references/source-notebook-map.md to see why sctour was split out from the shared trajectory skill.
• Read references/source-grounding.md for the current wrapper behavior and stored output keys.
• Read references/compatibility.md for dependency and validation limitations.