getStsDf: Obtain spatial trajectory screening data.frame

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain spatial trajectory screening data.frame

Description

Extracts a data.frame of inferred gradients related to the course of a trajectory.

Usage

getStsDf(
  object,
  variables,
  id = idST(object),
  resolution = recSgsRes(object),
  width = NULL,
  unit = getDefaultUnit(object),
  ro = c(0, 1),
  bcs_exclude = NULL,
  format = "wide",
  control = NULL,
  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.
variables	Character vector. All numeric variables to be included in the screening process.
resolution	Distance measure. The resolution with which the expression gradient is inferred. Defaults are platform specific. See more in detail section of recSgsRes().
width	Distance measure. The width of the trajectory frame. Defaults to the trajectory length.
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.
format	Character value. Either 'long' or 'wide'. Defaults to 'wide'. If 'wide' each variable gets a column. If 'long', the data.frame is organized such that a column called variables contains the variable names and a column called 'values' contains the values.
control	A list of arguments as taken from stats::loess.control(). Default setting is stored in SPATA2::sgs_loess_control.
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.