R/matrix_repeats.R

In dimitriskokoretsis/qpcrR:

#' @import data.table

.matrix_repeats <- function(m,value,use.line.names=TRUE) {

  if(typeof(m)!=typeof(value)) {
    stop("Error! Matrix and value should be of the same type.")
  }

  if(typeof(use.line.names)!="logical" | length(use.line.names)!=1) {
    stop("Error! use.line.names should be a logical vector (TRUE or FALSE) of length 1.")
  }

  line.names <- list(rows=NULL,cols=NULL)

  if(use.line.names==FALSE) {
    line.names$rows <- seq_len(nrow(m))
    line.names$cols <- seq_len(ncol(m))

  } else {
    if(is.null(rownames(m))) {
      rownames(m) <- as.character(seq_len(nrow(m)))
      line.names$rows <- rownames(m)

    } else {
      line.names$rows <- rownames(m)

    }

    if(is.null(colnames(m))) {
      colnames(m) <- as.character(seq_len(ncol(m)))
      line.names$cols <- colnames(m)

    } else {
      line.names$cols <- colnames(m)

    }
  }

  total.repeats <-

    mapply( # Apply over both the two orientations of the matrix (horizontal/vertical)
      function(m,value,margin,orientation.tag) {

        mapply( # Apply over EACH row or column (line) of matrix
          function(line,line.names,value,orientation.tag) {

            # Get the repeats in each line
            line <- line |>
              as.vector() |>
              .vector_repeats(value=value)

            # Write more information: name or number of column and orientation (horizontal/vertical)
            line[,c("row.or.column.name","orientation"):=
                   .(line.names,orientation.tag)]

            return(line)
          },
          line=asplit(m,margin),
          line.names=line.names[[margin]],
          SIMPLIFY=FALSE, # The SIMPLIFY=FALSE causes the result to be returned as a list
          MoreArgs=list(value=value, # This MoreArgs list passes the non-iterated elements in the function
                        orientation.tag=orientation.tag)
        ) |> rbindlist() # Binds the repeats of each individual row or column
      },
      margin=c(1,2),
      orientation.tag=as.factor(c("horizontal","vertical")),
      SIMPLIFY=FALSE, # The SIMPLIFY=FALSE causes the result to be returned as a list
      MoreArgs=list(m=m, # This MoreArgs list passes the non-iterated elements in the function
                    value=value)
    ) |> rbindlist() # Binds the repeats found in horizontal and vertical orientations

  if(use.line.names==TRUE) {
    total.repeats[,c("start","end"):=
                    .(fifelse(orientation=="horizontal",
                              line.names$cols[start],
                              line.names$rows[start]),
                      fifelse(orientation=="horizontal",
                              line.names$cols[end],
                              line.names$rows[end]))][]
  }

  return(total.repeats)

}