Run SecAct spatial signaling velocity

Run SecAct signaling velocity for spot-level ST or single-cell-resolution ST SpaCET objects.

Usage

RunSecActVelocity(
  SpaCET_obj,
  mode = c("spotST", "scST"),
  scale.factor = 1e+05,
  gene = NULL,
  signalMode = "receiving",
  radius = NULL,
  contourMap = FALSE,
  contourBins = 11,
  animated = FALSE,
  sender = NULL,
  secretedProtein = NULL,
  receiver = NULL,
  cellType_meta = NULL,
  CustomizedAreaCoordinates = NULL,
  show.coordinates = TRUE,
  colors = NULL,
  pointSize = 1,
  pointAlpha = 1,
  legend.position = "right",
  legend.size = 1,
  arrow.color = "#ff0099",
  arrow.width = 1,
  arrow.size = 0.3,
  verbose = TRUE
)

Arguments

SpaCET_obj

A SpaCET object.

mode

spotST calls SecAct.signaling.velocity.spotST; scST calls SecAct.signaling.velocity.scST.

scale.factor

Spot-level scale factor passed to SecAct.activity.inference.ST.

gene

Secreted protein gene used by spot-level ST velocity.

signalMode

receiving or sending for spot-level ST.

radius

Spatial radius. Defaults to 200 for spotST and 20 for scST when NULL.

contourMap, contourBins, animated

Plot options for spot-level ST.

sender, secretedProtein, receiver, cellType_meta

Parameters for scST velocity.

CustomizedAreaCoordinates, show.coordinates, colors, pointSize, pointAlpha, legend.position, legend.size, arrow.color, arrow.width, arrow.size

Plot options for scST velocity.

verbose

Whether to print the message. Default is TRUE.

Value

A ggplot object.