Secreted protein signaling velocity for single-cell ST

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,
  CustomizedAreaCoordinates = NULL,
  radius = 20,
  colors_cellType = NULL
)

Arguments

SpaCET_obj

A SpaCET object.

sender

Sender cell types.

secretedProtein

Secreted proteins.

receiver

Receiver cell types.

cellType_meta

Column name in meta data that includes cell-type annotations.

scale.factor

Sets the scale factor for spot-level normalization.

CustomizedAreaCoordinates

Optional coordinates for customized area c(x.left, x.right, y.bottom, y.top).

radius

Radius cut off (unit: um).

colors_cellType

Named vector of colors for cell types.

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

if (FALSE) { # \dontrun{
SecAct.signaling.velocity.scST(SpaCET_obj, sender="Fibroblast", 
  secretedProtein="THBS2", receiver="Tumor_boundary", cellType_meta="cellType")
} # }