improve ParseInput function

Add ability to pass in a data.table object and use S3 methods for ParseInput.
Fix up deprecated test context

DESCRIPTION

@@ -37,7 +37,7 @@ Suggests:
     devtools,
     knitr,
     rmarkdown
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 URL: https://ghar1821.github.io/TrackSOM/

NAMESPACE

@@ -9,7 +9,6 @@ export(TrackSOM)
 import(FlowSOM)
 import(RColorBrewer)
 import(data.table)
-import(flowCore)
 import(ggplot2)
 import(ggraph)
 import(gtools)
@@ -19,3 +18,4 @@ import(rlist)
 import(stringr)
 import(tidygraph)
 import(viridis)
+importFrom(flowCore,logicleTransform)

R/ParseInput.R

@@ -0,0 +1,248 @@
+#' S3 ParseInput function
+#' 
+#' Internal Function.
+#' Convert the input data to FlowSOM object ready to be processed.
+#' Many of the parameters are used by FlowSOM's ReadInput function.
+#' The description for these parameters are taken from FlowSOM.
+#' 
+#' @param inputFiles The list containing the input data
+#' @param compensate Whether to run data compensation
+#' @param spillover The spillover matrix to compensate
+#' @param transform Whether to run data transformation
+#' @param toTransform column names or indices to transform
+#' @param transformFunction The transform function to run
+#' @param scale Whether to scale the data
+#' @param scale.center See \link{base::scale}
+#' @param scale.scale See \link{base::scale}
+#' @param silent Whether to show progress updates
+#' @param colToUse Which column to be used by TrackSOM 
+#' @param ... Additional arguments used if inputFiles is a data.table object
+#' 
+#' @return FlowSOM object
+#' 
+ParseInput <- function(
+        inputFiles,
+        compensate,
+        spillover,
+        transform,
+        toTransform,
+        transformFunction,
+        scale,
+        scaled.center,
+        scaled.scale,
+        silent,
+        colsToUse,
+        ...
+    ) {
+    UseMethod("ParseInput")
+}
+
+#' @describeIn ParseInput Process vector of characters input
+#' 
+ParseInput.character <- function(
+        inputFiles,
+        compensate,
+        spillover,
+        transform,
+        toTransform,
+        transformFunction,
+        scale,
+        scaled.center,
+        scaled.scale,
+        silent,
+        colsToUse,
+        ...
+    ) {
+
+    # if it is a vector of filenames, it'll go to here.
+
+    inputFilesType <- unique(tools::file_ext(inputFiles))
+
+    if (length(inputFilesType) > 1) {
+        stop(paste(
+            "Multiple file types are detected (",
+            paste(inputFilesType, collapse = ", "),
+            "). Please pass only one file types in inputFiles!"
+        ))
+    }
+
+    inputFilesType <- inputFilesType[1]
+
+    if (! inputFilesType %in% c("fcs", "csv")) {
+        stop(paste(
+            "inputFiles are .", inputFilesType,
+            "file type. Only fcs or csv files are supported."
+        ))
+    }
+
+    if (inputFilesType == 'csv') {
+        data_ff <- lapply(inputFiles, function(input_file) {
+            input_dat <- fread(input_file)
+            input_dat_ff <-create_flowframe(input_dat, colsToUse)
+            return(input_dat_ff)
+        })
+        data_flowset <- as(data_ff, "flowSet")
+
+        fsom <- ReadInput(
+            data_flowset,
+            compensate  =  compensate,
+            spillover = spillover,
+            transform = transform,
+            toTransform = toTransform,
+            transformFunction = transformFunction,
+            scale = scale,
+            scaled.center = scaled.center,
+            scaled.scale = scaled.scale,
+            silent = silent
+        )
+    } else {
+        # will only get here if data files are fcs file
+        fsom <- ReadInput(
+            inputFiles,
+            pattern = ".fcs",
+            compensate  =  compensate,
+            spillover = spillover,
+            transform = transform,
+            toTransform = toTransform,
+            transformFunction = transformFunction,
+            scale = scale,
+            scaled.center = scaled.center,
+            scaled.scale = scaled.scale,
+            silent = silent
+        )
+    }
+
+    return(fsom)
+
+}
+
+#' @describeIn ParseInput Process list of data.frames input
+#' @import data.table
+#' 
+ParseInput.list <- function(
+        inputFiles,
+        compensate,
+        spillover,
+        transform,
+        toTransform,
+        transformFunction,
+        scale,
+        scaled.center,
+        scaled.scale,
+        silent,
+        colsToUse,
+        ...
+    ) {
+
+    # preliminary error checking
+    for (i in length(inputFiles)) {
+        if (! is.data.table(inputFiles[[i]])) {
+            stop(paste(
+                "element at position", i, 
+                "is not a data.table Please check."
+            ))
+        }
+    }
+
+    data_ff <- lapply(inputFiles, function(input_file) {
+        input_dat_ff <- create_flowframe(data.table(input_file), colsToUse)
+        return(input_dat_ff)
+    })
+    data_flowset <- as(data_ff, "flowSet")
+
+    fsom <- ReadInput(
+        data_flowset,
+        compensate  =  compensate,
+        spillover = spillover,
+        transform = transform,
+        toTransform = toTransform,
+        transformFunction = transformFunction,
+        scale = scale,
+        scaled.center = scaled.center,
+        scaled.scale = scaled.scale,
+        silent = silent
+    )
+
+    return(fsom)
+}
+
+#' @describeIn ParseInput Process data.table input
+#' @param timepoints A vector of time-points.
+#' @param timepointCol A character denoting the column in data.frame that
+#' corresponds to the time-point each cell belongs to
+#' 
+#' @import data.table
+#' 
+ParseInput.data.table <- function(
+        inputFiles,
+        compensate,
+        spillover,
+        transform,
+        toTransform,
+        transformFunction,
+        scale,
+        scaled.center,
+        scaled.scale,
+        silent,
+        colsToUse,
+        timepointCol,
+        timepoints
+) {
+    if (! timepointCol %in% names(inputFiles)) {
+        stop(paste(timepointCol, "column doesn't exist in inputFiles!"))
+    }
+
+    inputFiles <- data.table(inputFiles, keep.rownames = TRUE)
+
+    data_ff <- lapply(timepoints, function(t) {
+        input_dat <- inputFiles[get(timepointCol) == eval(t)]
+
+        input_dat_ff <- create_flowframe(input_dat, colsToUse)
+        return(input_dat_ff)
+    })
+    data_flowset <- as(data_ff, "flowSet")
+
+    fsom <- ReadInput(
+        data_flowset,
+        compensate  =  compensate,
+        spillover = spillover,
+        transform = transform,
+        toTransform = toTransform,
+        transformFunction = transformFunction,
+        scale = scale,
+        scaled.center = scaled.center,
+        scaled.scale = scaled.scale,
+        silent = silent
+    )
+
+    return(fsom)
+}
+
+#' Create flowframe
+#'
+#' @param input_dat a data.table
+#' @param colsToUse a vector of columns to isolate from input_dat
+#' 
+#' @import data.table
+#' 
+#' @return flowFrame object
+#' 
+create_flowframe <- function(input_dat, colsToUse) {
+    input_dat <- input_dat[, colsToUse, with = FALSE]
+
+    # convert to flowFrame. Pain in the butt
+    metadata <-
+        data.frame(
+            name = dimnames(input_dat)[[2]],
+            desc = paste('column', dimnames(input_dat)[[2]], 'from dataset')
+        )
+    # in order to create a flow frame, data (exprs param) needs to be read as
+    # matrix
+    input_dat_ff <- new(
+        "flowFrame",
+        exprs = as.matrix(input_dat),
+        parameters = Biobase::AnnotatedDataFrame(metadata)
+    )
+
+    return(input_dat_ff)
+}