R/projectFromNetworkRecombine.R

In BIMSBbioinfo/netSmooth: Network smoothing for scRNAseq

setGeneric(
  name = "projectFromNetworkRecombine",
  def = function(original_expression, smoothed_expression, filepath) {
    standardGeneric("projectFromNetworkRecombine")
  }
)

#' Combine gene expression from smoothed space (that of the network) with the
#' expression of genes that were not smoothed (not present in network)
#' @keywords internal
#' @param original_expression    the non-smoothed expression
#' @param smoothed_expression    the smoothed gene expression, in the space
#'                               of the genes defined by the network
#' @param filepath      String: Path to location where hdf5 output file is supposed to be saved.
#'                      Will be ignored when regular matrices or SummarizedExperiment are
#'                      used as input.
#' @return a matrix in the dimensions of original_expression, where values that
#'         are present in smoothed_expression are copied from there.
#' @importFrom data.table copy
setMethod("projectFromNetworkRecombine",
          signature(original_expression='matrix'),
          function(original_expression,
                   smoothed_expression) {
            data_in_original_space <- copy(original_expression)
            genes_in_both <- intersect(rownames(original_expression),
                                       rownames(smoothed_expression))
            data_in_original_space[genes_in_both,] <- as.matrix(
              smoothed_expression[genes_in_both,])
            return(data_in_original_space)
          })

setMethod("projectFromNetworkRecombine",
          signature(original_expression='Matrix'),
          function(original_expression,
                   smoothed_expression) {
            data_in_original_space <- copy(original_expression)
            genes_in_both <- intersect(rownames(original_expression),
                                       rownames(smoothed_expression))
            data_in_original_space[genes_in_both,] <- as.matrix(
              smoothed_expression[genes_in_both,])

            return(data_in_original_space)
          })

#' @importFrom HDF5Array writeHDF5Array
setMethod("projectFromNetworkRecombine",
          signature(original_expression='DelayedMatrix'),
          function(original_expression,
                   smoothed_expression,
                   filepath = NULL) {


            # genes in orignal and smoothed expression
            genes.in.both <- intersect(original_expression@seed@dimnames[[1]],
                                       rownames(smoothed_expression))

            # genes not in intersection
            original.exclusive <- original_expression@seed@dimnames[[1]][which(
              !(original_expression@seed@dimnames[[1]] %in% genes.in.both))]

            # use orignal expression as seed
            data_in_original_space <- writeHDF5Array(DelayedArray::DelayedArray(original_expression),
                                                     filepath = filepath)

            # set and row/col names and coerce to DelayedMatrix
            rownames(data_in_original_space) <- original_expression@seed@dimnames[[1]]
            colnames(data_in_original_space) <- original_expression@seed@dimnames[[2]]

            # replace rows in output
            data_in_original_space[genes.in.both,] <- smoothed_expression[genes.in.both,]

            return(data_in_original_space)
          })