Downstream analysis¶
scCS downstream analysis begins only after the supervised topology, ordering, velocity graph, anchor diagnostics, and future-fate sensitivity checks are acceptable.
Expression on the star¶
plot_gene_expression_star places measured expression on the same standardized
cell positions used for scCS metrics. It is a visualization of expression, not a
new scoring model. Use shared scales when comparing conditions and separate
scales when genes have very different dynamic ranges.
Expression trends¶
plot_expression_trends summarizes binned expression along ordering,
Conditional Fate Affinity, fate contribution, or Resolved Commitment. Binned
means are descriptive and should not be treated as independent observations.
Candidate commitment-associated genes¶
get_commitment_associated_genes estimates partial rank associations between
gene expression and a fitted scCS outcome.
inference_unit="cell_exploratory"is candidate generation only.inference_unit="replicate"aggregates biological replicate units before formal inference and is preferred when genuine replicate metadata exist.Association is not proof of a causal lineage driver.
Fate markers¶
get_fate_markers compares each annotated terminal population with the root.
These markers describe cell identity and are distinct from genes associated with
variation in future-fate commitment within the root.
Enrichment¶
run_commitment_enrichment accepts a local mapping or GMT file. Local gene
sets and an assay-specific background are preferred for publication-grade
reproducibility. Remote Enrichr libraries are optional and can change over time.
Interpretation order¶
A defensible downstream analysis reports:
velocity model and selected topology;
ordering and its validation;
DFFP parameters and anchor diagnostics;
CFA, DFR, FFS, RC, UFP, and SOF;
candidate genes or markers;
gene-set source, background, and enrichment thresholds;
biological replicate unit for any inferential claim.
See the pancreas and Schwann downstream-analysis tutorials for complete examples.