R/SpacoObject_constructor.R

In SPACO: Spatial Component Analysis for Spatial Sequencing Data

# Define a custom class for the object
setClass(
  "SpaCoObject",
  slots = c(
    neighbours = "Matrix",
    data = "matrix",
    coordinates = "data.frame",
    pixel_positions_list = "data.frame",
    data.dir = "character",
    slice = "character",
    spacs = "matrix",
    projection = "matrix",
    GraphLaplacian = "Matrix",
    Lambdas = "numeric",
    nSpacs = "integer",
    meta.data = "data.frame",
    denoised = "data.frame"
  )
)

#
#' Create a constructor function that creates an object of class SpaCoObject
#'
#' @param neighbours Binary matrix with weights describing if cells are to be considered neighbours or not depending on the defined distance.
#' @param data Matrix with normalized and scaled gene counts. Rows as cells and genes as columns
#' @param coordinates Matri with the cell coordinates on the slides. Rows and Columns in the 10x Visium case.
#' @return Returns a SpaCoObject with the given slots filled
#' @export
#'
#'
# Create a constructor function that creates an object of class SpaCoObject
# Define the custom class for the object
SpaCoObject <-
  function(neighbours,
           data,
           coordinates) {
    .check_SpaCo_inputs(as.list(environment()))
    new(
      "SpaCoObject",
      neighbours = Matrix::Matrix(neighbours),
      data = data,
      coordinates = coordinates,
      pixel_positions_list = new("data.frame"),
      data.dir = character(0),
      slice = character(0),
      spacs = new("matrix"),
      projection = new("matrix"),
      GraphLaplacian = Matrix::Matrix(numeric(0), 0, 0),
      Lambdas = numeric(0),
      nSpacs = integer(0),
      meta.data = new("data.frame"),
      denoised = new("data.frame")
    )
  }