@@ -125,6 +125,7 @@ import(grDevices)

 import(graphics)

 import(grid)

 import(uwot)

+importClassesFrom(Matrix,dgCMatrix)

 importClassesFrom(SingleCellExperiment,SingleCellExperiment)

 importFrom(MCMCprecision,fit_dirichlet)

 importFrom(Matrix,colSums)

@@ -353,7 +353,7 @@ setMethod(

 #'  matrix object.

 #' @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 caculating perplexity. Default \code{FALSE}.

+#' 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

@@ -134,6 +134,17 @@

 #' @param perplexity Logical. Whether to calculate perplexity for each model.

 #'  If FALSE, then perplexity can be calculated later with

 #'  \link{resamplePerplexity}. Default TRUE.

+#' @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}.

+#' 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.

@@ -162,6 +173,10 @@ setGeneric("recursiveSplitCell",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

     standardGeneric("recursiveSplitCell")})

@@ -205,6 +220,10 @@ setMethod("recursiveSplitCell",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

@@ -243,6 +262,10 @@ setMethod("recursiveSplitCell",

             reorder = reorder,

             seed = seed,

             perplexity = perplexity,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

@@ -311,6 +334,10 @@ setMethod("recursiveSplitCell",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         logfile = NULL,

         verbose = TRUE) {

@@ -340,6 +367,10 @@ setMethod("recursiveSplitCell",

             reorder = reorder,

             seed = seed,

             perplexity = perplexity,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

@@ -383,6 +414,10 @@ setMethod("recursiveSplitCell",

     reorder,

     seed,

     perplexity,

+    doResampling,

+    doSubsampling,

+    numResample,

+    numSubsample,

     logfile,

     verbose) {

@@ -400,6 +435,10 @@ setMethod("recursiveSplitCell",

             minCell = minCell,

             reorder = reorder,

             perplexity = perplexity,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample,

             logfile = logfile,

             verbose = verbose)

     } else {

@@ -418,6 +457,10 @@ setMethod("recursiveSplitCell",

                 minCell = minCell,

                 reorder = reorder,

                 perplexity = perplexity,

+                doResampling = doResampling,

+                doSubsampling = doSubsampling,

+                numResample = numResample,

+                numSubsample = numSubsample,

                 logfile = logfile,

                 verbose = verbose)

         )

@@ -440,6 +483,10 @@ setMethod("recursiveSplitCell",

                                minCell,

                                reorder,

                                perplexity,

+                               doResampling,

+                               doSubsampling,

+                               numResample,

+                               numSubsample,

                                logfile,

                                verbose) {

@@ -841,7 +888,11 @@ setMethod("recursiveSplitCell",

       verbose = verbose,

       logfile = NULL

     )

-    celdaRes <- resamplePerplexity(counts, celdaRes)

+    celdaRes <- resamplePerplexity(counts, celdaRes,

+                                   doResampling = doResampling,

+                                   doSubsampling = doSubsampling,

+                                   numResample = numResample,

+                                   numSubsample = numSubsample)

   }

   endTime <- Sys.time()

   .logMessages(

@@ -918,7 +969,18 @@ setMethod("recursiveSplitCell",

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

 #' @param perplexity Logical. Whether to calculate perplexity for each model.

 #'  If FALSE, then perplexity can be calculated later with

-#'  \link{resamplePerplexity}. Default TRUE.

+#'  \link{resamplePerplexity}. Default \code{TRUE}.

+#' @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}.

+#' 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.

@@ -947,6 +1009,10 @@ setGeneric("recursiveSplitModule",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

     standardGeneric("recursiveSplitModule")})

@@ -983,6 +1049,10 @@ setMethod("recursiveSplitModule",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

@@ -1021,6 +1091,10 @@ setMethod("recursiveSplitModule",

             reorder = reorder,

             seed = seed,

             perplexity = perplexity,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample,

             verbose = verbose,

             logfile = logfile)

@@ -1082,6 +1156,10 @@ setMethod("recursiveSplitModule",

         reorder = TRUE,

         seed = 12345,

         perplexity = TRUE,

+        doResampling = FALSE,

+        doSubsampling = TRUE,

+        numResample = 5,

+        numSubsample = 5000,

         verbose = TRUE,

         logfile = NULL) {

@@ -1111,6 +1189,10 @@ setMethod("recursiveSplitModule",

             reorder = reorder,

             seed = seed,

             perplexity = perplexity,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample,

             verbose = verbose,

             logfile = logfile)

@@ -1154,6 +1236,10 @@ setMethod("recursiveSplitModule",

     reorder,

     seed,

     perplexity,

+    doResampling,

+    doSubsampling,

+    numResample,

+    numSubsample,

     verbose,

     logfile) {

@@ -1173,7 +1259,11 @@ setMethod("recursiveSplitModule",

             reorder = reorder,

             perplexity = perplexity,

             verbose = verbose,

-            logfile = logfile)

+            logfile = logfile,

+            doResampling = doResampling,

+            doSubsampling = doSubsampling,

+            numResample = numResample,

+            numSubsample = numSubsample)

     } else {

         with_seed(seed,

             celdaList <- .recursiveSplitModule(

@@ -1191,7 +1281,11 @@ setMethod("recursiveSplitModule",

                 reorder = reorder,

                 perplexity = perplexity,

                 verbose = verbose,

-                logfile = logfile)

+                logfile = logfile,

+                doResampling = doResampling,

+                doSubsampling = doSubsampling,

+                numResample = numResample,

+                numSubsample = numSubsample)

         )

     }

@@ -1213,7 +1307,11 @@ setMethod("recursiveSplitModule",

                                  reorder = TRUE,

                                  perplexity = TRUE,

                                  verbose = TRUE,

-                                 logfile = NULL) {

+                                 logfile = NULL,

+                                 doResampling = FALSE,

+                                 doSubsampling = TRUE,

+                                 numResample = 5,

+                                 numSubsample = 5000) {

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

     logfile = logfile,

@@ -1573,7 +1671,11 @@ setMethod("recursiveSplitModule",

       verbose = verbose,

       logfile = NULL

     )

-    celdaRes <- resamplePerplexity(counts, celdaRes)

+    celdaRes <- resamplePerplexity(counts, celdaRes,

+                                   doResampling = doResampling,

+                                   doSubsampling = doSubsampling,

+                                   numResample = numResample,

+                                   numSubsample = numSubsample)

   }

   endTime <- Sys.time()

new file mode 100644

@@ -0,0 +1,19 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{eigenMatMultInt}

+\alias{eigenMatMultInt}

+\title{Fast matrix multiplication for double x int}

+\usage{

+eigenMatMultInt(A, B)

+}

+\arguments{

+\item{A}{a double matrix}

+

+\item{B}{an integer matrix}

+}

+\value{

+An integer matrix representing the product of A and B

+}

+\description{

+Fast matrix multiplication for double x int

+}

new file mode 100644

@@ -0,0 +1,19 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{eigenMatMultNumeric}

+\alias{eigenMatMultNumeric}

+\title{Fast matrix multiplication for double x double}

+\usage{

+eigenMatMultNumeric(A, B)

+}

+\arguments{

+\item{A}{a double matrix}

+

+\item{B}{an integer matrix}

+}

+\value{

+An integer matrix representing the product of A and B

+}

+\description{

+Fast matrix multiplication for double x double

+}

new file mode 100644

@@ -0,0 +1,19 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{fastNormProp}

+\alias{fastNormProp}

+\title{Fast normalization for numeric matrix}

+\usage{

+fastNormProp(R_counts, R_alpha)

+}

+\arguments{

+\item{R_counts}{An integer matrix}

+

+\item{R_alpha}{A double value to be added to the matrix as a pseudocount}

+}

+\value{

+A numeric matrix where the columns have been normalized to proportions

+}

+\description{

+Fast normalization for numeric matrix

+}

new file mode 100644

@@ -0,0 +1,19 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{fastNormPropLog}

+\alias{fastNormPropLog}

+\title{Fast normalization for numeric matrix}

+\usage{

+fastNormPropLog(R_counts, R_alpha)

+}

+\arguments{

+\item{R_counts}{An integer matrix}

+

+\item{R_alpha}{A double value to be added to the matrix as a pseudocount}

+}

+\value{

+A numeric matrix where the columns have been normalized to proportions

+}

+\description{

+Fast normalization for numeric matrix

+}

new file mode 100644

@@ -0,0 +1,19 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{fastNormPropSqrt}

+\alias{fastNormPropSqrt}

+\title{Fast normalization for numeric matrix}

+\usage{

+fastNormPropSqrt(R_counts, R_alpha)

+}

+\arguments{

+\item{R_counts}{An integer matrix}

+

+\item{R_alpha}{A double value to be added to the matrix as a pseudocount}

+}

+\value{

+A numeric matrix where the columns have been normalized to proportions

+}

+\description{

+Fast normalization for numeric matrix

+}

new file mode 100644

@@ -0,0 +1,17 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/RcppExports.R

+\name{nonzero}

+\alias{nonzero}

+\title{get row and column indices of none zero elements in the matrix}

+\usage{

+nonzero(R_counts)

+}

+\arguments{

+\item{R_counts}{A matrix}

+}

+\value{

+An integer matrix where each row is a row, column indices pair

+}

+\description{

+get row and column indices of none zero elements in the matrix

+}

@@ -23,6 +23,10 @@ recursiveSplitCell(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -44,6 +48,10 @@ recursiveSplitCell(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -65,6 +73,10 @@ recursiveSplitCell(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   logfile = NULL,

   verbose = TRUE

 )

@@ -135,6 +147,21 @@ a default value of 12345 is used. If NULL, no calls to

 If FALSE, then perplexity can be calculated later with

 \link{resamplePerplexity}. Default TRUE.}

+\item{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}.}

+

+\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}.

+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.}

@@ -23,6 +23,10 @@ recursiveSplitModule(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -44,6 +48,10 @@ recursiveSplitModule(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -65,6 +73,10 @@ recursiveSplitModule(

   reorder = TRUE,

   seed = 12345,

   perplexity = TRUE,

+  doResampling = FALSE,

+  doSubsampling = TRUE,

+  numResample = 5,

+  numSubsample = 5000,

   verbose = TRUE,

   logfile = NULL

 )

@@ -128,7 +140,22 @@ a default value of 12345 is used. If NULL, no calls to

 \item{perplexity}{Logical. Whether to calculate perplexity for each model.

 If FALSE, then perplexity can be calculated later with

-\link{resamplePerplexity}. Default TRUE.}

+\link{resamplePerplexity}. Default \code{TRUE}.}

+

+\item{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}.}

+

+\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}.

+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.}

@@ -59,7 +59,7 @@ to use. Default "featureSubset".}

 \item{doResampling}{Boolean. If \code{TRUE}, then each cell in the counts

 matrix will be resampled according to a multinomial distribution to introduce

-noise before caculating perplexity. Default \code{FALSE}.}

+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}.}