Secreted protein signaling velocity — SecAct.signaling.velocity.spotST • SecAct

Calculate the signaling velocity of secreted proteins based on their activities.

Usage

SecAct.signaling.velocity.spotST(
  SpaCET_obj,
  scale.factor = 1e+05,
  gene,
  signalMode = "receiving",
  animated = FALSE
)

Arguments

SpaCET_obj: A SpaCET object.
scale.factor: Sets the scale factor for spot-level normalization.
gene: Gene symbol coding a secreted protein.
signalMode: Mode of signaling velocity, i.e., "receiving", "sending", and "both".
animated: A logical indicating whether generate animated figure.

Value

A ggplot2 object.

Details

The velocity direction starts from the source cell producing a secreted protein and moves to sink cells receiving the secreted protein signal. The velocity magnitude represents the product between the secreted protein-coding gene expression at source cells and signaling activities at sink cells.

Examples

SecAct.signaling.velocity.spotST(SpaCET_obj, gene="TGFB1", signalMode="receiving")
SecAct.signaling.velocity.spotST(SpaCET_obj, gene="TGFB1", signalMode="sending")
SecAct.signaling.velocity.spotST(SpaCET_obj, gene="TGFB1", signalMode="both")