@@ -10,7 +10,7 @@

   # Patch delayed decorator.

   if (! is.null({pretty_patched = attr(decorator, 'calls')}))

     pretty_decorators = c(pretty_patched, pretty_decorators[-1])

-  

+

   # Handle operator precedence so that we can chain decorators.

   if (inherits(f, 'decorator'))

     .delayed_decorate(decorator, f, pretty_decorators)

@@ -29,7 +29,7 @@ print.decorated = function (x, useSource = TRUE, ...) {

     attr(bare, 'decorators') = NULL

     bare

   }

-  

+

   fun_def = utils::capture.output(print.function(bare(x), useSource = useSource, ...))

   for (decorator in attr(x, 'decorators'))

     cat(deparse(decorator), '%@%\n')

@@ -54,11 +54,12 @@ pretty_code = function (f) {

 .delayed_decorate = function (d1, d2, decorator_calls)

   structure(decorator(function (f) d1(d2(f))), calls = decorator_calls)

-#' 

+#'

 #' @name simpleLog

 #' @title A decorator that prints the arguments to the decorated function

 #' @param f A function to decorate

-#' 

+#' @return Prints message

+#'

 simpleLog <- decorator %@% function(f) {

   function(...) {

     message(deparse(match.call()))

@@ -18,6 +18,7 @@

 #' @param compressionOpts Integer. Sets the compression level

 #' @param forceDense Default \code{False} Write sparse data as a dense matrix.

 #' Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.

+#' @return Generates a Python anndata object containing data from \code{inSCE}.

 #' @examples

 #' data(sce_chcl, package = "scds")

 #' exportSCEtoAnnData(sce=sce_chcl, compression="gzip")

@@ -11,6 +11,7 @@

 #'  gzip compressed. \code{FALSE} otherwise. Default

 #'  \code{TRUE}.

 #' @param sample Name of the sample. It will be used as the prefix of file names.

+#' @return Generates text files containing data from \code{inSCE}.

 #' @examples

 #' data(sce_chcl, package = "scds")

 #' exportSCEtoFlatFile(sce_chcl, "sce_chcl")

@@ -37,6 +37,7 @@

 #'  68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.}

 #' }

 #' @author Joshua D. Campbell, David Jenkins

+#' @return The specified \link[SingleCellExperiment]{SingleCellExperiment} object.

 #' @examples

 #' sce <- importExampleData("pbmc3k")

 #' @export

@@ -35,6 +35,9 @@

 #' \link{importGeneSetsFromCollection} for importing from

 #' \linkS4class{GeneSetCollection} objects, and

 #' \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets.

+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

+#'  with gene set from \code{collectionName} output stored to the

+#'  \link[SummarizedExperiment]{metadata} slot.

 #' @examples

 #' data(scExample)

 #'

@@ -87,6 +90,9 @@ importGeneSetsFromGMT <- function(inSCE, file,

 #' can point to different locations within \code{inSCE}. See

 #' \link{featureIndex} for more information.

 #' Default \code{"rownames"}.

+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

+#' with gene set from \code{collectionName} output stored to the

+#' \link[SummarizedExperiment]{metadata} slot.

 #' @details The gene identifiers in gene sets in \code{geneSetList} will be

 #' mapped to the rownames of \code{inSCE} using the \code{by} parameter and

 #' stored in a \linkS4class{GeneSetCollection} object from package

@@ -182,6 +188,9 @@ importGeneSetsFromList <- function(inSCE, geneSetList,

 #' in the \code{GeneSetCollection}.

 #' See \link{featureIndex} for more information.

 #' Default \code{"rownames"}.

+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

+#' with gene set from \code{collectionName} output stored to the

+#' \link[SummarizedExperiment]{metadata} slot.

 #' @details The gene identifiers in gene sets in the

 #' \code{GeneSetCollection} will be mapped to the rownames of

 #' \code{inSCE} using the \code{by} parameter and

@@ -304,6 +313,9 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection,

 #' of \code{inSCE}. See \link{featureIndex} for more information.

 #' Default \code{"rownames"}.

 #' @param verbose Boolean. Whether to display progress. Default \code{TRUE}.

+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object

+#' with gene set from \code{collectionName} output stored to the

+#' \link[SummarizedExperiment]{metadata} slot.

 #' @details The gene identifiers in gene sets from MSigDB will be retrieved

 #' using the \code{\link{msigdbr}} package. They will be mapped to the IDs in

 #' \code{inSCE} using the \code{by} parameter and

@@ -420,6 +432,7 @@ importGeneSetsFromMSigDB <- function(inSCE, categoryIDs,

 #' @description Returns a vector of GeneSetCollections that have been

 #' imported and stored in \code{metadata(inSCE)$sctk$genesets}.

 #' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object.

+#' @return Character vector.

 #' @author Joshua D. Campbell

 #' @seealso \link{importGeneSetsFromList} for importing from lists,

 #' \link{importGeneSetsFromGMT} for importing from GMT files,

@@ -456,6 +469,7 @@ sctkListGeneSetCollections <- function(inSCE) {

 #' @description Returns a data.frame that shows MSigDB categories and

 #' subcategories as well as descriptions for each. The entries in the ID

 #' column in this table can be used as input for \link{importGeneSetsFromMSigDB}.

+#' @return data.frame, containing MSigDB categories

 #' @author Joshua D. Campbell

 #' @seealso \link{importGeneSetsFromMSigDB} for importing MSigDB gene sets.

 #' @export

@@ -6,6 +6,7 @@

 #' used when running a differential expression analysis function.

 #' @param labelBy A single character for a column of \code{rowData(inSCE)} as

 #' where to search for the labeling text. Default \code{NULL}.

+#' @return Stop point if found

 .checkDiffExpResultExists <- function(inSCE, useResult, labelBy = NULL){

   if(!inherits(inSCE, 'SingleCellExperiment')){

     stop('Given object is not a valid SingleCellExperiment object.')

@@ -43,6 +43,7 @@

 #' @param rowIndexLocation Character. For Optimus output, The path to the

 #'  feature (gene) index .npy file. Used only if \code{file} has .npz extension.

 #'  Default \code{NULL}.

+#' @return A \link[DelayedArray]{DelayedArray} object or matrix.

 #' @examples

 #' mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/",

 #'     "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))

@@ -44,6 +44,7 @@ ad <- NULL

 #'        to install via pip due to compilation requirements).

 #' @param pythonVersion Passed to \code{python_version} variable in \code{\link[reticulate]{conda_install}}. Default NULL.

 #' @param ... Other parameters to pass to \code{\link[reticulate]{conda_install}}.

+#' @return None. Installation of Conda environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallConda(envname = "sctk-reticulate")

@@ -93,6 +94,7 @@ sctkPythonInstallConda <- function(envname = "sctk-reticulate",

 #' @param packages Character Vector. List of packages to install.

 #' @param selectEnvironment Boolean. Run \code{\link[singleCellTK]{selectSCTKVirtualEnvironment}} after installing all packages to select the virtual environment. Default TRUE.

 #' @param python The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

+#' @return None. Installation of virtual environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")

@@ -124,6 +126,7 @@ sctkPythonInstallVirtualEnv <- function(envname = "sctk-reticulate",

 #' @title Selects a Conda environment

 #' @description Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}.

 #' @param envname Character. Name of the conda environment to activate.

+#' @return None. Selects Conda environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallConda(envname = "sctk-reticulate", selectConda = FALSE)

@@ -157,6 +160,7 @@ selectSCTKConda <- function(envname = "sctk-reticulate") {

 #' @title Selects a virtual environment

 #' @description Selects a virtual environment with Python packages used in \code{\link{singleCellTK}}

 #' @param envname Character. Name of the virtual environment to activate.

+#' @return None. Selects virtual environment.

 #' @examples

 #' \dontrun{

 #' sctkPythonInstallVirtualEnv(envname = "sctk-reticulate", selectEnvironment = FALSE)

@@ -106,16 +106,19 @@

     return(df)

 }

-#' @title Plot table of SCTK QC outputs.

-#' @description Plot QC metrics generated from QC algorithms via either kable or csv file.

+#' @title Generate table of SCTK QC outputs.

+#' @description  Creates a table of QC metrics generated from

+#'  QC algorithms via either kable or csv file.

 #' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved

-#' dimension reduction components or a variable with saved results. Required

+#' \link[SummarizedExperiment]{assay} data and/or

+#' \link[SummarizedExperiment]{colData} data. Required.

 #' @param sample Character vector. Indicates which sample each cell belongs to.

 #' @param useAssay  A string specifying which assay in the SCE to use. Default

 #'  'counts'.

 #' @param simple Boolean. Indicates whether to generate a table of only

 #' basic QC stats (ex. library size), or to generate a summary table of all

 #' QC stats stored in the inSCE.

+#' @return A matrix/array object.

 #' @examples

 #' data(scExample, package = "singleCellTK")

 #' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

@@ -9,6 +9,7 @@

 #' @param directory Output directory. Default is './'.

 #' @param format The format of output. It currently supports flat files, rds files

 #' and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").

+#' @return Generates a file containing data from \code{inSCE} as \code{format}.

 #' @examples

 #' exportSCE(mouseBrainSubsetSCE, format = "SCE")

 #' @export

@@ -190,6 +191,7 @@ generateMeta <- function(dropletSCE = NULL,

 #' @param samplename The sample name of the \link[SingleCellExperiment]{SingleCellExperiment} objects.

 #' @param writeYAML Whether output yaml file to store parameters. Default if TRUE. If FALSE,

 #' return character object.

+#' @return If \code{writeYAML} TRUE, a yaml object will be generated. If FALSE, character object.

 #' @export

 getSceParams <- function(inSCE,

                          skip = c("scrublet", "runDecontX","runBarcodeRanksMetaOutput"),

@@ -493,6 +493,8 @@ seuratHeatmapPlot <- function(plotObject, dims, ncol, labels) {

 #' @param assaySlotSCE Selected assay to update in the input SingleCellExperiment object

 #' @param seuratDataSlot Selected data slot from the Seurat object. Default \code{"counts"}.

 #' @param seuratAssaySlot Selected assay from Seurat object. Default \code{"RNA"}.

+#' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with

+#'  data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.

 #' @importFrom SummarizedExperiment assay<-

 .updateAssaySCE <- function(inSCE, seuratObject, assaySlotSCE, seuratDataSlot = "counts", seuratAssaySlot = "RNA") {

   assay(inSCE, assaySlotSCE) <- NULL

@@ -17,6 +17,9 @@ used when running a differential expression analysis function.}

 \item{labelBy}{A single character for a column of \code{rowData(inSCE)} as

 where to search for the labeling text. Default \code{NULL}.}

 }

+\value{

+Stop point if found

+}

 \description{

 Check if the specified MAST result in SingleCellExperiment object is

 complete. But does not garantee the biological correctness.

@@ -24,6 +24,10 @@ Update/Modify/Add an assay in the provided SingleCellExperiment object from a Se

 \item{seuratAssaySlot}{Selected assay from Seurat object. Default \code{"RNA"}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object with

+ data from Seurat object appended to the \link[SummarizedExperiment]{assay} slot.

+}

 \description{

 .updateAssaySCE

 Update/Modify/Add an assay in the provided SingleCellExperiment object from a Seurat object

@@ -28,6 +28,9 @@ It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}

 \item{format}{The format of output. It currently supports flat files, rds files

 and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").}

 }

+\value{

+Generates a file containing data from \code{inSCE} as \code{format}.

+}

 \description{

 Export data in SingleCellExperiment object

 }

@@ -38,6 +38,9 @@ Default \code{"counts"}.}

 \item{forceDense}{Default \code{False} Write sparse data as a dense matrix.

 Refer \code{anndata.write_h5ad} documentation for details. Default \code{NULL}.}

 }

+\value{

+Generates a Python anndata object containing data from \code{inSCE}.

+}

 \description{

 Writes all assays, colData, rowData, reducedDims, and altExps objects in a

 \link[SingleCellExperiment]{SingleCellExperiment} to a Python annData object in the .h5ad format

@@ -27,6 +27,9 @@ gzip compressed. \code{FALSE} otherwise. Default

 \item{sample}{Name of the sample. It will be used as the prefix of file names.}

 }

+\value{

+Generates text files containing data from \code{inSCE}.

+}

 \description{

 Writes all assays, colData, rowData, reducedDims, and altExps objects in a

 \link[SingleCellExperiment]{SingleCellExperiment} to text files.

@@ -6,6 +6,9 @@

 \usage{

 getMSigDBTable()

 }

+\value{

+data.frame, containing MSigDB categories

+}

 \description{

 Returns a data.frame that shows MSigDB categories and

 subcategories as well as descriptions for each. The entries in the ID

@@ -28,6 +28,9 @@ getSceParams(

 \item{writeYAML}{Whether output yaml file to store parameters. Default if TRUE. If FALSE,

 return character object.}

 }

+\value{

+If \code{writeYAML} TRUE, a yaml object will be generated. If FALSE, character object.

+}

 \description{

 Extract QC parameters from the SingleCellExperiment object

 }

@@ -18,6 +18,9 @@ will store the data as a sparse matrix from package \link{Matrix} while

 \item{delayedArray}{Boolean. Whether to read the expression matrix as

 \link[DelayedArray]{DelayedArray} object or not. Default \code{FALSE}.}

 }

+\value{

+The specified \link[SingleCellExperiment]{SingleCellExperiment} object.

+}

 \description{

 Retrieves published example datasets stored in

 \link[SingleCellExperiment]{SingleCellExperiment} using the

@@ -37,6 +37,11 @@ in the \code{GeneSetCollection}.

 See \link{featureIndex} for more information.

 Default \code{"rownames"}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object

+with gene set from \code{collectionName} output stored to the

+\link[SummarizedExperiment]{metadata} slot.

+}

 \description{

 Converts a list of gene sets stored in a

 \linkS4class{GeneSetCollection} object and stores it in the metadata of the

@@ -39,6 +39,11 @@ Default \code{"rownames"}.}

 \item{sep}{Character. Delimiter of the GMT file. Default \code{"\t"}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object

+ with gene set from \code{collectionName} output stored to the

+ \link[SummarizedExperiment]{metadata} slot.

+}

 \description{

 Converts a list of gene sets stored in a GMT file into a

 \linkS4class{GeneSetCollection} and stores it in the metadata of the

@@ -36,6 +36,11 @@ can point to different locations within \code{inSCE}. See

 \link{featureIndex} for more information.

 Default \code{"rownames"}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object

+with gene set from \code{collectionName} output stored to the

+\link[SummarizedExperiment]{metadata} slot.

+}

 \description{

 Converts a list of gene sets into a

 \linkS4class{GeneSetCollection} and stores it in the metadata of the

@@ -39,6 +39,11 @@ Default \code{"rownames"}.}

 \item{verbose}{Boolean. Whether to display progress. Default \code{TRUE}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object

+with gene set from \code{collectionName} output stored to the

+\link[SummarizedExperiment]{metadata} slot.

+}

 \description{

 Gets a list of MSigDB gene sets stores it in the metadata of the

 \linkS4class{SingleCellExperiment} object. These gene sets can be used in

@@ -33,6 +33,9 @@ Default \code{NULL}.}

 feature (gene) index .npy file. Used only if \code{file} has .npz extension.

 Default \code{NULL}.}

 }

+\value{

+A \link[DelayedArray]{DelayedArray} object or matrix.

+}

 \description{

 Automatically detact the format of the input file and read

  the file.

@@ -2,13 +2,14 @@

 % Please edit documentation in R/sampleSummaryStats.R

 \name{sampleSummaryStats}

 \alias{sampleSummaryStats}

-\title{Plot table of SCTK QC outputs.}

+\title{Generate table of SCTK QC outputs.}

 \usage{

 sampleSummaryStats(inSCE, sample = NULL, useAssay = "counts", simple = TRUE)

 }

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved

-dimension reduction components or a variable with saved results. Required}

+\link[SummarizedExperiment]{assay} data and/or

+\link[SummarizedExperiment]{colData} data. Required.}

 \item{sample}{Character vector. Indicates which sample each cell belongs to.}

@@ -19,8 +20,12 @@ dimension reduction components or a variable with saved results. Required}

 basic QC stats (ex. library size), or to generate a summary table of all

 QC stats stored in the inSCE.}

 }

+\value{

+A matrix/array object.

+}

 \description{

-Plot QC metrics generated from QC algorithms via either kable or csv file.

+Creates a table of QC metrics generated from

+ QC algorithms via either kable or csv file.

 }

 \examples{

 data(scExample, package = "singleCellTK")

@@ -9,6 +9,9 @@ sctkListGeneSetCollections(inSCE)

 \arguments{

 \item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object.}

 }

+\value{

+Character vector.

+}

 \description{

 Returns a vector of GeneSetCollections that have been

 imported and stored in \code{metadata(inSCE)$sctk$genesets}.

@@ -37,6 +37,9 @@ to install via pip due to compilation requirements).}

 \item{...}{Other parameters to pass to \code{\link[reticulate]{conda_install}}.}

 }

+\value{

+None. Installation of Conda environment.

+}

 \description{

 Install all Python packages used in the \code{\link{singleCellTK}} package

 using \code{\link[reticulate]{conda_install}} from package \code{\link{reticulate}}. This

@@ -21,6 +21,9 @@ sctkPythonInstallVirtualEnv(

 \item{python}{The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.}

 }

+\value{

+None. Installation of virtual environment.

+}

 \description{

 Install all Python packages used in the \code{\link{singleCellTK}} package

 using \code{\link[reticulate]{virtualenv_install}} from package \code{\link{reticulate}}. This

@@ -9,6 +9,9 @@ selectSCTKConda(envname = "sctk-reticulate")

 \arguments{

 \item{envname}{Character. Name of the conda environment to activate.}

 }

+\value{

+None. Selects Conda environment.

+}

 \description{

 Selects a Conda environment with Python packages used in \code{\link{singleCellTK}}.

 }

@@ -9,6 +9,9 @@ selectSCTKVirtualEnvironment(envname = "sctk-reticulate")

 \arguments{

 \item{envname}{Character. Name of the virtual environment to activate.}

 }

+\value{

+None. Selects virtual environment.

+}

 \description{

 Selects a virtual environment with Python packages used in \code{\link{singleCellTK}}

 }

@@ -9,6 +9,9 @@ simpleLog(f)

 \arguments{

 \item{f}{A function to decorate}

 }

+\value{

+Prints message

+}

 \description{

 A decorator that prints the arguments to the decorated function

 }

@@ -25,10 +25,14 @@ then \code{"x < 5"} will return all columns with x less than 5.

 Single quotes should be used for character strings. For example,

 \code{"y == 'yes'"} will return all columns where y is "yes".

 Multiple expressions can be evaluated by placing them in a vector.

-For example \code{c("x < 5", "y =='yes'")} will apply both operations for 

+For example \code{c("x < 5", "y =='yes'")} will apply both operations for

 subsetting. If \code{NULL}, this will not be used for subsetting.

 Default \code{NULL}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object that has

+been subsetted by colData.

+}

 \description{

 Used to peform subsetting of a

 \linkS4class{SingleCellExperiment} object using a variety of methods that

@@ -38,7 +42,7 @@ with one another.

 }

 \examples{

 data(scExample)

-sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")                          

+sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 }

 \author{

 Joshua D. Campbell

@@ -29,14 +29,14 @@ for subsetting. Default \code{NULL}.}

 \item{rowData}{Character. An expression that will identify a subset of rows

 using variables found in the \code{rowData} of \code{inSCE}. For example,

 if \code{x} is a numeric vector in \code{rowData}, then \code{"x < 5"} will

-return all rows with x less than 5. Single quotes should be used for 

+return all rows with x less than 5. Single quotes should be used for

 character strings. For example, \code{"y == 'yes'"} will return all

 rows where y is "yes". Multiple expressions can be evaluated by placing them

 in a vector. For example \code{c("x < 5", "y =='yes'")} will apply both

 operations for subsetting. If \code{NULL}, this will not be used for

 subsetting. Default \code{NULL}.}

-\item{returnAsAltExp}{Boolean. If \code{TRUE}, the subsetted 

+\item{returnAsAltExp}{Boolean. If \code{TRUE}, the subsetted

 \linkS4class{SingleCellExperiment} object will be returned in the

 \code{altExp} slot of \code{inSCE}. If \code{FALSE}, the subsetted

 \linkS4class{SingleCellExperiment} object will be directly returned.}

@@ -48,6 +48,10 @@ add if \code{returnAsAltExp = TRUE}. Default \code{subset}.}

 be added to the beginning of the assay names in the \code{altExp} object.

 This is only utilized if \code{returnAsAltExp = TRUE}. Default \code{TRUE}.}

 }

+\value{

+A \link[SingleCellExperiment]{SingleCellExperiment} object that has

+been subsetted by rowData.

+}

 \description{

 Used to peform subsetting of a

 \linkS4class{SingleCellExperiment} object using a variety of methods that

@@ -64,7 +68,7 @@ data(scExample)

 # Set a variable up in the rowData indicating mitochondrial genes

 rowData(sce)$isMito <- ifelse(grepl("^MT-", rowData(sce)$feature_name),

                               "yes", "no")

-sce <- subsetSCERows(sce, rowData = "isMito == 'yes'")                          

+sce <- subsetSCERows(sce, rowData = "isMito == 'yes'")

 }

 \author{

 Joshua D. Campbell