Run SecAct spatial signaling pattern analysis — RunSecActSignalingPattern • scop

Run SecAct.signaling.pattern on a SpaCET object with existing SecAct activity results.

Usage

RunSecActSignalingPattern(
  SpaCET_obj,
  scale.factor = 1e+05,
  radius = 200,
  k,
  verbose = TRUE
)

Arguments

SpaCET_obj: A SpaCET object.
scale.factor: Spot-level scale factor passed to SecAct.activity.inference.ST.
radius: Radius cutoff.
k: Number of NMF patterns, or candidate pattern numbers.
verbose: Whether to print the message. Default is TRUE.

Value

A SpaCET object with SecAct signaling pattern results.