Gradient Tocky Sequence (Slerp Model)

Projects cells onto a piecewise Slerp manifold defined by the landmarks B -> BR -> R. Cells with negative correlations to all three landmarks are classified as "Timer Negative" (NA), as they lie in the ordination space opposite to the Tocky trajectory.

Usage

GradientTockySeq(res, B, BR, R, filter_negative = TRUE)

Arguments

res

List object returned by CanonicalTockySeq (must contain $cell_scores coordinates).

B

Vector for the 'New' (Blue) landmark.

BR

Vector for the 'Persistent' (Blue-Red) landmark.

R

Vector for the 'Arrested' (Red) landmark.

filter_negative

Logical. If TRUE, assigns NA to cells with negative projection to all three landmarks.

Value

A data frame containing:

angle

Tocky Time (0-90)

intensity

Raw Euclidean norm (distance from origin)

norm_intensity

Intensity normalized against the Slerp trajectory

similarity

Cosine similarity to the manifold