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

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

Usage

SecAct.signaling.velocity.scST(
  SpaCET_obj,
  sender,
  secretedProtein,
  receiver,
  cellType_meta,
  scale.factor = 1e+05,
  radius = 0.02
)

Arguments

SpaCET_obj: A SpaCET object.
sender: Sender cell types.
secretedProtein: Secreted proteins.
receiver: Receiver cell types.
scale.factor: Sets the scale factor for spot-level normalization.

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.scST(SpaCET_obj, sender="Fibroblast", secretedProtein="THBS2", receiver="Tumor_boundary", cellType_meta="cellType")