R/apply.R

In moritzlindner/PatchR: An environment for working with ephys (PatchClamp) recordings

#' apply function for PRecording objects
#'
#' `r lifecycle::badge("experimental")` \cr
#' This is the PatchR analog to \code{apply}
#'
#' @param X A \linkS4class{PRecording}  object
#' @param MARGIN A vector giving the subscripts which the function will be applied along. Understands \code{Time}, \code{Sweep},\code{Trace}, or \code{1-3} resp.
#' @param FUN The function to be applied
#' @param ReturnPObject Whether to return results as a \linkS4class{PRecording} with an additional, computed trace only works with \code{MARGIN="Trace"} or if applying \code{FUN} leaves dimensions unchanged. Default is \var{FALSE}, then returns a matrix.
#' @param Verbose Print what function is doing.
#' @seealso \link[base:apply]{base::apply()}
#' @return A \link[base:matrix]{matrix}  or \linkS4class{PRecording} object.
#' @exportMethod apply
setMethod("apply",
          "PRecording",
          function(X,
                   MARGIN,
                   FUN,
                   ReturnPObject = F,
                   Verbose = T) {
            # translate Margins
            if (is.character(MARGIN)) {
              MARG <- MARGIN
              if (MARGIN == "Time") {
                MARGIN <- 1
              }
              if (MARGIN == "Sweep") {
                MARGIN <- 2
              }
              if (MARGIN == "Trace") {
                MARGIN <- 3
              }
            } else{
              if (MARGIN == 1) {
                MARG <- "Time"
              }
              if (MARGIN == 2) {
                MARG <- "Sweep"
              }
              if (MARGIN == 3) {
                MARG <- "Trace"
              }
            }
            
            if (!(MARGIN %in% c(1:3))) {
              stop("Undefined MARGIN selected")
            }
            
            if (Verbose) {
              message(paste(
                "Function ",
                paste(eval(deparse(FUN)), collapse = ''),
                " applied along",
                MARG
              ))
            }
            
            #simplify and apply
            DAT <- simplify2array(X@Data)
            margins <- 1:length(dim(DAT))
            
            #out <- apply(DAT, margins[!(margins %in% MARGIN)], FUN)
            if (is.character(FUN)) {
              if (FUN %in% unlist(lapply(c("Arith"), getGroupMembers))) {
                if (MARGIN == 1) {
                  out <- get(FUN)(DAT[1, ], DAT[2, ])
                }
                if (MARGIN == 2) {
                  message("Untested operation!")
                  out <- get(FUN)(DAT[, 1], DAT[, 1])
                }
              } else{
                stop("FUN not supported")
              }
            } else{
              out <- apply(DAT, margins[!(margins %in% MARGIN)], FUN)
            }
            
            if (isTRUE(all.equal(dim(out), dim(DAT)))) {
              dimnames(out) <- dimnames(DAT)
              if (ReturnPObject) {
                warning("Updating data in PRecording!")
                out <-
                  lapply(seq(dim(out)[3]), function(y)
                    out[, , y])
                names(out) <- names(X@Data)
                X@Data <- out
                out <- X
              }
            } else{
              if (MARGIN == 1) {
                if (!ReturnPObject) {
                  colnames(out) <- GetTraceNames(X)
                  rownames(out) <- GetSweepNames(X)
                } else{
                  warning("Updating data in PRecording!")
                  Data <- t(out)
                  Data <-
                    lapply(seq_len(nrow(Data)), function(i)
                      Data[i, ])
                  names(Data) <- GetTraceNames(X)
                  Data <- lapply(Data, function(x) {
                    t(as.matrix(x))
                  })
                  out <- PatchR:::PRecording(
                    Traces = GetTraceNames(X),
                    Units = X@Units,
                    TimeTrace = as.numeric(NA),
                    TimeUnit = X@TimeUnit,
                    Sweeps = X@Sweeps,
                    SweepTimes = X@SweepTimes,
                    Data = Data,
                    Plots = list(),
                    RecordingParams = X@RecordingParams
                  )
                }
              }
              if (MARGIN == 2) {
                if (!ReturnPObject) {
                  out <- cbind(X@TimeTrace, out)
                  colnames(out) <-
                    c(paste0("Time [", X@TimeUnit, "]"), GetTraceNames(X))
                } else{
                  warning("Updating data in PRecording!")
                  Data <-
                    lapply(seq_len(ncol(out)), function(i)
                      out[, i])
                  names(Data) <- GetTraceNames(X)
                  Data <- lapply(Data, as.matrix)
                  for (i in seq_along(Data)) {
                    colnames(Data[[i]]) <- make.names(deparse1(FUN, collapse = ""))
                  }
                  out <- PRecording(
                    Traces = GetTraceNames(X),
                    Units = X@Units,
                    TimeTrace = X@TimeTrace,
                    TimeUnit = X@TimeUnit,
                    Sweeps = ordered(make.names(deparse1(
                      FUN, collapse = ""
                    ))),
                    SweepTimes = 0,
                    Data = Data,
                    Plots = list(),
                    RecordingParams = X@RecordingParams
                  )
                  
                }
              }
              if (MARGIN == 3) {
                if (!ReturnPObject) {
                  out <- cbind(X@TimeTrace, out)
                  colnames(out) <-
                    c(paste0("Time [", X@TimeUnit, "]"), GetSweepNames(X))
                } else{
                  X <-
                    AddTrace(
                      X = X,
                      Trace = make.names(deparse1(FUN, collapse = "")),
                      Unit = "NA",
                      mtx = out
                    )
                  out <- X
                }
              }
            }
            return(out)
          })