@@ -354,14 +354,9 @@ setMethod(

 #' @param doResampling Boolean. If \code{TRUE}, then each cell in the counts

 #' matrix will be resampled according to a multinomial distribution to introduce

 #' noise before calculating perplexity. Default \code{FALSE}.

-#' @param doSubsampling Boolean. If \code{TRUE}, then a subset of cells from

-#' the original counts matrix will be randomly selected. Default \code{TRUE}.

 #' @param numResample Integer. The number of times to resample the counts matrix

-#' for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+#' for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 #' Default \code{5}.

-#' @param numSubsample Integer. The number of cells to sample from the

-#' the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-#' Default \code{5000}.

 #' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,

 #'  a default value of \code{12345} is used. If \code{NULL}, no calls to

 #'  \link[withr]{with_seed} are made.

@@ -376,9 +371,7 @@ setGeneric("resamplePerplexity",

         useAssay = "counts",

         altExpName = "featureSubset",

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         seed = 12345) {

     standardGeneric("resamplePerplexity")})

@@ -395,9 +388,7 @@ setMethod("resamplePerplexity",

         useAssay = "counts",

         altExpName = "featureSubset",

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         seed = 12345) {

         altExp <- SingleCellExperiment::altExp(x, altExpName)

@@ -409,18 +400,14 @@ setMethod("resamplePerplexity",

                 counts = counts,

                 celdaList = celdaList,

                 doResampling = doResampling,

-                doSubsampling = doSubsampling,

-                numResample = numResample,

-                numSubsample = numSubsample)

+                numResample = numResample)

         } else {

             with_seed(seed,

                 res <- .resamplePerplexity(

                     counts = counts,

                     celdaList = celdaList,

                     doResampling = doResampling,

-                    doSubsampling = doSubsampling,

-                    numResample = numResample,

-                    numSubsample = numSubsample))

+                    numResample = numResample))

         }

         S4Vectors::metadata(altExp)$celda_grid_search <- res

@@ -444,9 +431,7 @@ setMethod("resamplePerplexity",

     function(x,

         celdaList,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         seed = 12345) {

         if (is.null(seed)) {

@@ -454,18 +439,14 @@ setMethod("resamplePerplexity",

                 counts = x,

                 celdaList = celdaList,

                 doResampling = doResampling,

-                doSubsampling = doSubsampling,

-                numResample = numResample,

-                numSubsample = numSubsample)

+                numResample = numResample)

         } else {

             with_seed(seed,

                 res <- .resamplePerplexity(

                     counts = x,

                     celdaList = celdaList,

                     doResampling = doResampling,

-                    doSubsampling = doSubsampling,

-                    numResample = numResample,

-                    numSubsample = numSubsample))

+                    numResample = numResample))

         }

         return(res)

@@ -476,9 +457,7 @@ setMethod("resamplePerplexity",

 .resamplePerplexity <- function(counts,

     celdaList,

     doResampling = FALSE,

-    doSubsampling = TRUE,

-    numResample = 5,

-    numSubsample = 5000) {

+    numResample = 5) {

     if (!methods::is(celdaList, "celdaList")) {

         stop("celdaList parameter was not of class celdaList.")

@@ -486,31 +465,17 @@ setMethod("resamplePerplexity",

     if (!isTRUE(is.logical(doResampling))) {

         stop("The 'doResampling' parameter needs to be logical (TRUE/FALSE).")

     } 

-    if (!isTRUE(is.logical(doSubsampling))) {

-        stop("The 'doSubsampling' parameter needs to be logical (TRUE/FALSE).")

-    } 

     if (!isTRUE(doResampling) & (!is.numeric(numResample) || numResample < 1)) {

         stop("The 'numResample' parameter needs to be an integer greater ",

         "than 0.")

     }

-    if (!isTRUE(doSubsampling) & (!is.numeric(numSubsample) || numSubsample < 1)) {

-        stop("The 'numResample' parameter needs to be an integer between ",

-             "1 and the number of cells.")

-    }

-    if(isTRUE(doSubsampling) & numSubsample < ncol(counts)) {

-        ix <- sample(seq(ncol(counts)), size = numSubsample)

-        newCounts <- counts[,ix]

-        

-    } else {

-        newCounts <- counts

-    }

     if(isTRUE(doResampling)) {

         perpRes <- matrix(NA,

                           nrow = length(resList(celdaList)),

                           ncol = numResample)

         for (j in seq(numResample)) {

-            newCounts <- .resampleCountMatrix(newCounts)

+            newCounts <- .resampleCountMatrix(counts)

             for (i in seq(length(resList(celdaList)))) {

                 perpRes[i, j] <- perplexity(x = counts,

                     celdaMod = resList(celdaList)[[i]],

@@ -526,7 +491,7 @@ setMethod("resamplePerplexity",

         for (i in seq(length(resList(celdaList)))) {

             perpRes[i,1] <- perplexity(x = counts,

                                        celdaMod = resList(celdaList)[[i]],

-                                       newCounts = newCounts)

+                                       newCounts = counts)

         }

     }    

@@ -137,14 +137,9 @@

 #' @param doResampling Boolean. If \code{TRUE}, then each cell in the counts

 #' matrix will be resampled according to a multinomial distribution to introduce

 #' noise before calculating perplexity. Default \code{FALSE}.

-#' @param doSubsampling Boolean. If \code{TRUE}, then a subset of cells from

-#' the original counts matrix will be randomly selected. Default \code{TRUE}.

 #' @param numResample Integer. The number of times to resample the counts matrix

-#' for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+#' for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 #' Default \code{5}.

-#' @param numSubsample Integer. The number of cells to sample from the

-#' the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-#' Default \code{5000}.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

 #' @param logfile Character. Messages will be redirected to a file named

 #'  "logfile". If NULL, messages will be printed to stdout.  Default NULL.

@@ -174,9 +169,7 @@ setGeneric("recursiveSplitCell",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

     standardGeneric("recursiveSplitCell")})

@@ -221,9 +214,7 @@ setMethod("recursiveSplitCell",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

@@ -263,9 +254,7 @@ setMethod("recursiveSplitCell",

             seed = seed,

             perplexity = perplexity,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

             numResample = numResample,

-            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

@@ -335,9 +324,7 @@ setMethod("recursiveSplitCell",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

@@ -368,9 +355,7 @@ setMethod("recursiveSplitCell",

             seed = seed,

             perplexity = perplexity,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

             numResample = numResample,

-            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

@@ -415,9 +400,7 @@ setMethod("recursiveSplitCell",

     seed,

     perplexity,

     doResampling,

-    doSubsampling,

     numResample,

-    numSubsample,

     logfile,

     verbose) {

@@ -436,9 +419,7 @@ setMethod("recursiveSplitCell",

             reorder = reorder,

             perplexity = perplexity,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

             numResample = numResample,

-            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

     } else {

@@ -458,9 +439,7 @@ setMethod("recursiveSplitCell",

                 reorder = reorder,

                 perplexity = perplexity,

                 doResampling = doResampling,

-                doSubsampling = doSubsampling,

                 numResample = numResample,

-                numSubsample = numSubsample,

                 logfile = logfile,

                 verbose = verbose)

         )

@@ -484,9 +463,7 @@ setMethod("recursiveSplitCell",

                                reorder,

                                perplexity,

                                doResampling,

-                               doSubsampling,

                                numResample,

-                               numSubsample,

                                logfile,

                                verbose) {

@@ -890,9 +867,7 @@ setMethod("recursiveSplitCell",

     )

     celdaRes <- resamplePerplexity(counts, celdaRes,

                                    doResampling = doResampling,

-                                   doSubsampling = doSubsampling,

-                                   numResample = numResample,

-                                   numSubsample = numSubsample)

+                                   numResample = numResample)

   }

   endTime <- Sys.time()

   .logMessages(

@@ -973,14 +948,9 @@ setMethod("recursiveSplitCell",

 #' @param doResampling Boolean. If \code{TRUE}, then each cell in the counts

 #' matrix will be resampled according to a multinomial distribution to introduce

 #' noise before calculating perplexity. Default \code{FALSE}.

-#' @param doSubsampling Boolean. If \code{TRUE}, then a subset of cells from

-#' the original counts matrix will be randomly selected. Default \code{TRUE}.

 #' @param numResample Integer. The number of times to resample the counts matrix

-#' for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+#' for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 #' Default \code{5}.

-#' @param numSubsample Integer. The number of cells to sample from the

-#' the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-#' Default \code{5000}.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

 #' @param logfile Character. Messages will be redirected to a file named

 #'  "logfile". If NULL, messages will be printed to stdout.  Default NULL.

@@ -1010,9 +980,7 @@ setGeneric("recursiveSplitModule",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

     standardGeneric("recursiveSplitModule")})

@@ -1050,9 +1018,7 @@ setMethod("recursiveSplitModule",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

@@ -1092,9 +1058,7 @@ setMethod("recursiveSplitModule",

             seed = seed,

             perplexity = perplexity,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

             numResample = numResample,

-            numSubsample = numSubsample,

             verbose = verbose,

             logfile = logfile)

@@ -1157,9 +1121,7 @@ setMethod("recursiveSplitModule",

         seed = 12345,

         perplexity = TRUE,

         doResampling = FALSE,

-        doSubsampling = TRUE,

         numResample = 5,

-        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

@@ -1190,9 +1152,7 @@ setMethod("recursiveSplitModule",

             seed = seed,

             perplexity = perplexity,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

             numResample = numResample,

-            numSubsample = numSubsample,

             verbose = verbose,

             logfile = logfile)

@@ -1237,9 +1197,7 @@ setMethod("recursiveSplitModule",

     seed,

     perplexity,

     doResampling,

-    doSubsampling,

     numResample,

-    numSubsample,

     verbose,

     logfile) {

@@ -1261,9 +1219,7 @@ setMethod("recursiveSplitModule",

             verbose = verbose,

             logfile = logfile,

             doResampling = doResampling,

-            doSubsampling = doSubsampling,

-            numResample = numResample,

-            numSubsample = numSubsample)

+            numResample = numResample)

     } else {

         with_seed(seed,

             celdaList <- .recursiveSplitModule(

@@ -1283,9 +1239,7 @@ setMethod("recursiveSplitModule",

                 verbose = verbose,

                 logfile = logfile,

                 doResampling = doResampling,

-                doSubsampling = doSubsampling,

-                numResample = numResample,

-                numSubsample = numSubsample)

+                numResample = numResample)

         )

     }

@@ -1309,9 +1263,7 @@ setMethod("recursiveSplitModule",

                                  verbose = TRUE,

                                  logfile = NULL,

                                  doResampling = FALSE,

-                                 doSubsampling = TRUE,

-                                 numResample = 5,

-                                 numSubsample = 5000) {

+                                 numResample = 5) {

   .logMessages(paste(rep("=", 50), collapse = ""),

     logfile = logfile,

@@ -1673,9 +1625,7 @@ setMethod("recursiveSplitModule",

     )

     celdaRes <- resamplePerplexity(counts, celdaRes,

                                    doResampling = doResampling,

-                                   doSubsampling = doSubsampling,

-                                   numResample = numResample,

-                                   numSubsample = numSubsample)

+                                   numResample = numResample)

   }

   endTime <- Sys.time()

@@ -24,9 +24,7 @@ recursiveSplitCell(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -49,9 +47,7 @@ recursiveSplitCell(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -74,9 +70,7 @@ recursiveSplitCell(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -151,17 +145,10 @@ If FALSE, then perplexity can be calculated later with

 matrix will be resampled according to a multinomial distribution to introduce

 noise before calculating perplexity. Default \code{FALSE}.}

-\item{doSubsampling}{Boolean. If \code{TRUE}, then a subset of cells from

-the original counts matrix will be randomly selected. Default \code{TRUE}.}

-

 \item{numResample}{Integer. The number of times to resample the counts matrix

-for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 Default \code{5}.}

-\item{numSubsample}{Integer. The number of cells to sample from the

-the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-Default \code{5000}.}

-

 \item{logfile}{Character. Messages will be redirected to a file named

 "logfile". If NULL, messages will be printed to stdout.  Default NULL.}

@@ -24,9 +24,7 @@ recursiveSplitModule(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -49,9 +47,7 @@ recursiveSplitModule(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -74,9 +70,7 @@ recursiveSplitModule(

   seed = 12345,

   perplexity = TRUE,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -146,17 +140,10 @@ If FALSE, then perplexity can be calculated later with

 matrix will be resampled according to a multinomial distribution to introduce

 noise before calculating perplexity. Default \code{FALSE}.}

-\item{doSubsampling}{Boolean. If \code{TRUE}, then a subset of cells from

-the original counts matrix will be randomly selected. Default \code{TRUE}.}

-

 \item{numResample}{Integer. The number of times to resample the counts matrix

-for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 Default \code{5}.}

-\item{numSubsample}{Integer. The number of cells to sample from the

-the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-Default \code{5000}.}

-

 \item{verbose}{Logical. Whether to print log messages. Default TRUE.}

 \item{logfile}{Character. Messages will be redirected to a file named

@@ -12,9 +12,7 @@ resamplePerplexity(

   useAssay = "counts",

   altExpName = "featureSubset",

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   seed = 12345

 )

@@ -23,9 +21,7 @@ resamplePerplexity(

   useAssay = "counts",

   altExpName = "featureSubset",

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   seed = 12345

 )

@@ -33,9 +29,7 @@ resamplePerplexity(

   x,

   celdaList,

   doResampling = FALSE,

-  doSubsampling = TRUE,

   numResample = 5,

-  numSubsample = 5000,

   seed = 12345

 )

 }

@@ -61,17 +55,10 @@ to use. Default "featureSubset".}

 matrix will be resampled according to a multinomial distribution to introduce

 noise before calculating perplexity. Default \code{FALSE}.}

-\item{doSubsampling}{Boolean. If \code{TRUE}, then a subset of cells from

-the original counts matrix will be randomly selected. Default \code{TRUE}.}

-

 \item{numResample}{Integer. The number of times to resample the counts matrix

-for evaluating perplexity if \code{doSubsampling} is set to \code{TRUE}.

+for evaluating perplexity if \code{doResampling} is set to \code{TRUE}.

 Default \code{5}.}

-\item{numSubsample}{Integer. The number of cells to sample from the

-the counts matrix if \code{doSubsampling} is set to \code{TRUE}. 

-Default \code{5000}.}

-

 \item{seed}{Integer. Passed to \link[withr]{with_seed}. For reproducibility,

 a default value of \code{12345} is used. If \code{NULL}, no calls to

 \link[withr]{with_seed} are made.}