Obtain spatial annotation screening data.frame

Extracts a data.frame of inferred gradients of numeric variables as a function of distance to spatial annotations.

getSasDf(
  object,
  ids,
  distance = "dte",
  resolution = recSgsRes(object),
  core = FALSE,
  angle_span = c(0, 360),
  n_bins_angle = 1,
  variables = NULL,
  unit = getDefaultUnit(object),
  ro = c(0, 1),
  format = "wide",
  bcs_exclude = character(0),
  outlier_rm = FALSE,
  verbose = FALSE,
  ...
)

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

ids

Character vector. Specifies the IDs of the spatial annotations of interest.

distance

Distance measure. Specifies the distance from the border of the spatial annotation to the horizon in the periphery up to which the screening is conducted. Defaults to a distance that covers the whole tissue section the spatial annotation is located on using distToEdge(). (This distance must not be exceeded.)

resolution

Distance measure. The resolution with which the expression gradient is inferred. Defaults are platform specific. See more in detail section of recSgsRes().

angle_span

Numeric vector of length 2. Confines the area screened by an angle span relative to the center of its closest spatial annotation.

variables

Character vector. The numeric variables to be included in the screening process. Makre sure that the correct matrix is active in the respective assays.

unit

Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.

ro

The numeric range to which the output gradients is scaled. Defaults to c(0,1).

bcs_exclude

Character value containing the barcodes of observations to be excluded from the analysis.

outlier_rm

Deprecated.

verbose

Logical. If TRUE, informative messages regarding the computational progress will be printed.

(Warning messages will always be printed.)

...

Used to absorb deprecated arguments or functions.

Value

Data.frame.