getSasDf: Obtain spatial annotation screening data.frame

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain spatial annotation screening data.frame

Description

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

Usage

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.

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.