@@ -36,6 +36,7 @@ export(getDEGTopTable)

 export(getGenesetNamesFromCollection)

 export(getMSigDBTable)

 export(getPathwayResultNames)

+export(getSampleSummaryStats)

 export(getSceParams)

 export(getTSNE)

 export(getTopHVG)

@@ -2,7 +2,7 @@

                                 simple = TRUE){

     metrics <- c("Number of Cells")

-    values <- c(ncol(inSCE))

+    values <- c(as.integer(ncol(inSCE)))

     if ("sum" %in% colnames(SummarizedExperiment::colData(inSCE))) {

         metrics <- c(metrics, "Mean counts", "Median counts")

@@ -107,7 +107,8 @@

 #' @title Generate table of SCTK QC outputs.

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

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

+#'  QC algorithms, which is stored within the metadata slot of the

+#'  input SingleCellExperiment object.

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

 #' \link{assay} data and/or \link{colData} data. Required.

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

@@ -116,11 +117,13 @@

 #' @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.

+#' @return A SingleCellExperiment object with a summary table for QC statistics

+#' in the `sampleSummary` slot of metadata.

 #' @examples

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

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

-#' sampleSummaryStats(sce, simple = TRUE)

+#' sce <- sampleSummaryStats(sce, simple = TRUE)

+#' getSampleSummaryStats(sce)

 #' @importFrom magrittr %>%

 #' @export

 sampleSummaryStats <- function(inSCE,

@@ -179,5 +182,60 @@ sampleSummaryStats <- function(inSCE,

         return((signif(x,5)))

     })

-    return(dfTableRes)

+    inSCE <- setSampleSummaryStats(inSCE, slot = "sctk_qc",

+                                   stats = dfTableRes)

+    return(inSCE)

 }

+

+

+#' @title Store table of SCTK QC outputs to metadata. Executed within

+#' `sampleSummaryStats` function.

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

+#'  QC algorithms within the metadata slot of the SingleCellExperiment object.

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

+#' \link{assay} data and/or \link{colData} data. Required.

+#' @param slot A \code{character} value which specifies the

+#' desired slot to store the stats table within the metadata of

+#' the SingleCellExperiment object. Required.

+#' @param stats Input stats table that will be stored within the

+#' SingleCellExperiment object. Required.

+#' @return A SingleCellExperiment object with a summary table for QC statistics

+#' in the `sampleSummary` slot of metadata.

+setSampleSummaryStats <- function(inSCE,

+                                  slot,

+                                  stats){

+    inSCE@metadata$sctk$sampleSummary[[slot]] <- stats

+    return(inSCE)

+}

+

+#' @title Store table of SCTK QC outputs to metadata.

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

+#'  QC algorithms within the metadata slot of the SingleCellExperiment object.

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

+#' \link{assay} data and/or \link{colData} data. Required.

+#' @param slot A \code{character} value indicating the slot

+#' that stores the stats table within the metadata of the

+#' SingleCellExperiment object. Required.

+#' @return A matrix/array object. Contains a summary table for QC statistics

+#' generated from SingleCellTK.

+#' @export

+#' @examples

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

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

+#' sce <- runCellQC(sce)

+#' sce <- sampleSummaryStats(sce, simple = FALSE)

+#' getSampleSummaryStats(sce, slot = "sctk_qc")

+getSampleSummaryStats <- function(inSCE, slot){

+    if(missing(slot)){ # If slot parameter is missing, then return first element.

+        return(inSCE@metadata$sctk$sampleSummary[[1]])

+    }

+

+    if(!is.null(inSCE@metadata$sctk$sampleSummary[[slot]])){

+        return(inSCE@metadata$sctk$sampleSummary[[slot]])

+    }

+    else{

+        #Return error with message

+        stop("Please run the `sampleSummaryStats` function first to generate

+             the QC statistics summary table.")

+    }

+}

\ No newline at end of file

@@ -559,7 +559,7 @@ for(i in seq_along(process)) {

             for (name in names(metadata(mergedFilteredSCE))) {

                 if (name != "assayType") {

                     metadata(mergedFilteredSCE)[[name]] <- list(metadata(mergedFilteredSCE)[[name]])

-                    names(metadata(mergedFilteredSCE)[[name]]) <- samplename                    

+                    names(metadata(mergedFilteredSCE)[[name]]) <- samplename

                 }

             }

         }

@@ -596,7 +596,8 @@ for(i in seq_along(process)) {

             reportCellQC(inSCE = mergedFilteredSCE, output_dir = directory, output_file = paste0("SCTK_", samplename,'_cellQC.html'), subTitle = subTitle, studyDesign = studyDesign)

             ## generate QC metrics table for mergedFilteredSCE

-            QCsummary <- sampleSummaryStats(mergedFilteredSCE, simple=FALSE, sample = colData(mergedFilteredSCE)$sample) #colData(cellSCE)$Study_ID

+            mergedFilteredSCE <- sampleSummaryStats(mergedFilteredSCE, simple=FALSE, sample = colData(mergedFilteredSCE)$sample) #colData(cellSCE)$Study_ID

+            QCsummary <- getSampleSummaryStats(mergedFilteredSCE, slot = "sctk_qc")

             write.csv(QCsummary, file.path(directory,

                                            samplename,

                                            paste0("SCTK_", samplename,'_cellQC_summary.csv')))

@@ -647,7 +648,8 @@ for(i in seq_along(process)) {

                          samplename = samplename, writeYAML = TRUE,

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

-            QCsummary <- sampleSummaryStats(mergedFilteredSCE, simple=FALSE, sample = colData(mergedFilteredSCE)$sample) #colData(cellSCE)$Study_ID

+            mergedFilteredSCE <- sampleSummaryStats(mergedFilteredSCE, simple=FALSE, sample = colData(mergedFilteredSCE)$sample) #colData(cellSCE)$Study_ID

+            QCsummary <- getSampleSummaryStats(mergedFilteredSCE, slot = "sctk_qc")

             write.csv(QCsummary, file.path(directory,

                                            samplename,

                                            paste0("SCTK_", samplename,'_cellQC_summary.csv')))

@@ -688,7 +690,7 @@ if (!isTRUE(split)) {

                 if (name != "assayType") {

                     names(metadata(cellSCE)[[name]]) <- sample

                 }

-            }            

+            }

         }

         exportSCE(inSCE = dropletSCE, samplename = samplename, directory = directory, type = "Droplets", format=formats)

@@ -719,7 +721,8 @@ if (!isTRUE(split)) {

         }

         ## generate QC summary

-        QCsummary <- sampleSummaryStats(cellSCE, simple=FALSE, sample = colData(cellSCE)$sample)

+        cellSCE <- sampleSummaryStats(cellSCE, simple=FALSE, sample = colData(cellSCE)$sample)

+        QCsummary <- getSampleSummaryStats(cellSCE, slot = "sctk_qc")

         write.csv(QCsummary, file.path(directory,

                                        samplename,

                                        paste0("SCTK_", samplename,'_cellQC_summary.csv')))

@@ -733,7 +736,7 @@ if (!isTRUE(split)) {

             for (name in names(metadata(cellSCE))) {

               if (name != "assayType") {

                   metadata(cellSCE)[[name]] <- list(metadata(cellSCE)[[name]])

-                  names(metadata(cellSCE)[[name]]) <- samplename                

+                  names(metadata(cellSCE)[[name]]) <- samplename

               }

             }

         } else {

@@ -744,7 +747,7 @@ if (!isTRUE(split)) {

                 if (name != "assayType") { ### not important and hard to force name. Skipped

                     names(metadata(cellSCE)[[name]]) <- sample

                 }

-            }            

+            }

         }

         exportSCE(inSCE = cellSCE, samplename = samplename, directory = directory, type = "Cells", format=formats)

@@ -767,7 +770,8 @@ if (!isTRUE(split)) {

         reportCellQC(inSCE = cellSCE, output_dir = directory, output_file = paste0("SCTK_", samplename,'_cellQC.html'), subTitle = subTitle, studyDesign = studyDesign)

         getSceParams(inSCE = cellSCE, directory = directory, samplename = samplename, writeYAML = TRUE)

-        QCsummary <- sampleSummaryStats(cellSCE, simple=FALSE, sample = colData(cellSCE)$sample)

+        cellSCE <- sampleSummaryStats(cellSCE, simple=FALSE, sample = colData(cellSCE)$sample)

+        QCsummary <- getSampleSummaryStats(cellSCE, slot = "sctk_qc")

         write.csv(QCsummary, file.path(directory,

                                        samplename,

                                        paste0("SCTK_", samplename,'_cellQC_summary.csv')))

@@ -139,10 +139,11 @@ description_runPerCellQC <- descriptionRunPerCellQC()

 ```{r "SummaryStats", echo = FALSE, results="asis", fig.align="center", warning=FALSE, message=FALSE}

 cat("\n")

-summaryTable <- sampleSummaryStats(inSCE = sce.qc, 

+sce.qc <- sampleSummaryStats(inSCE = sce.qc, 

                                    sample = sceSample,

                                    simple = FALSE)

+summaryTable <- getSampleSummaryStats(sce.qc, slot = "sctk_qc")

 cat(apply(summaryTable, 1:2, as.character) %>% 

     knitr::kable(format = "html") %>%

       kableExtra::kable_styling() %>%

new file mode 100644

@@ -0,0 +1,31 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/sampleSummaryStats.R

+\name{getSampleSummaryStats}

+\alias{getSampleSummaryStats}

+\title{Store table of SCTK QC outputs to metadata.}

+\usage{

+getSampleSummaryStats(inSCE, slot)

+}

+\arguments{

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

+\link{assay} data and/or \link{colData} data. Required.}

+

+\item{slot}{A \code{character} value indicating the slot

+that stores the stats table within the metadata of the

+SingleCellExperiment object. Required.}

+}

+\value{

+A matrix/array object. Contains a summary table for QC statistics

+generated from SingleCellTK.

+}

+\description{

+Stores a table of QC metrics generated from

+ QC algorithms within the metadata slot of the SingleCellExperiment object.

+}

+\examples{

+data(scExample, package = "singleCellTK")

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

+sce <- runCellQC(sce)

+sce <- sampleSummaryStats(sce, simple = FALSE)

+getSampleSummaryStats(sce, slot = "sctk_qc")

+}

@@ -20,14 +20,17 @@ 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.

+A SingleCellExperiment object with a summary table for QC statistics

+in the `sampleSummary` slot of metadata.

 }

 \description{

 Creates a table of QC metrics generated from

- QC algorithms via either kable or csv file.

+ QC algorithms, which is stored within the metadata slot of the

+ input SingleCellExperiment object.

 }

 \examples{

 data(scExample, package = "singleCellTK")

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

-sampleSummaryStats(sce, simple = TRUE)

+sce <- sampleSummaryStats(sce, simple = TRUE)

+getSampleSummaryStats(sce)

 }

new file mode 100644

@@ -0,0 +1,28 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/sampleSummaryStats.R

+\name{setSampleSummaryStats}

+\alias{setSampleSummaryStats}

+\title{Store table of SCTK QC outputs to metadata. Executed within

+`sampleSummaryStats` function.}

+\usage{

+setSampleSummaryStats(inSCE, slot, stats)

+}

+\arguments{

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

+\link{assay} data and/or \link{colData} data. Required.}

+

+\item{slot}{A \code{character} value which specifies the

+desired slot to store the stats table within the metadata of

+the SingleCellExperiment object. Required.}

+

+\item{stats}{Input stats table that will be stored within the

+SingleCellExperiment object. Required.}

+}

+\value{

+A SingleCellExperiment object with a summary table for QC statistics

+in the `sampleSummary` slot of metadata.

+}

+\description{

+Stores a table of QC metrics generated from

+ QC algorithms within the metadata slot of the SingleCellExperiment object.

+}

@@ -13,8 +13,12 @@ test_that("summarizeSCE", {

 test_that(desc = "Testing sampleSummaryStats", {

   data(scExample)

-  stats <- sampleSummaryStats(sce, simple = FALSE)

-  expect_true("matrix" %in% class(stats))

+  sce <- sampleSummaryStats(sce, simple = FALSE)

+  expect_true("sctk" %in% names(metadata(sce)))

+  expect_is(metadata(sce)$sctk$sample_summary$sctk_qc,

+            "matrix")

+  expect_is(getSampleSummaryStats(sce, slot = "sctk_qc"),

+            "matrix")

 })

@@ -131,16 +131,18 @@ reducedDims(pbmc.combined)

 #### Generating a summary statistic table

-The function `sampleSummaryStats()` may be used to generate a table containing the mean and median of the data per sample. 

+The function `sampleSummaryStats()` may be used to generate a table containing the mean and median of the data per sample, which is stored within the `sctk_qc` table under `metadata`. The table can then be returned using `getSampleSummaryStats`.

 ```{r sampleSummaryStats}

-sampleSummaryStats(pbmc.combined, sample = sample.vector)

+pbmc.combined <- sampleSummaryStats(pbmc.combined, sample = sample.vector)

+getSampleSummaryStats(pbmc.combined, slot = "sctk_qc")

 ```

 If users choose to generate a table for all QC metrics generated through `runCellQC()`, they may set the `simple` parameter to `FALSE`.

 ```{r sampleSummaryStatsQC}

-sampleSummaryStats(pbmc.combined, sample = sample.vector, simple = FALSE)

+pbmc.combined <- sampleSummaryStats(pbmc.combined, sample = sample.vector, simple = FALSE)

+getSampleSummaryStats(pbmc.combined, slot = "sctk_qc")

 ```

 ### Running individual QC methods