@@ -79,7 +79,7 @@

   ## Get merged rowData

   by.r <- unique(c('rownames', by.r))

-  unionFe <- Reduce(function(r1, r2) merge(r1, r2, by=by.r, all=T), feList)

+  unionFe <- Reduce(function(r1, r2) merge(r1, r2, by=by.r, all=TRUE), feList)

   allGenes <- unique(unlist(lapply(feList, rownames)))

   ## rowData

@@ -104,7 +104,7 @@

   })

   by.c <- unique(c("rownames", by.c))

-  unionCb <- Reduce(function(c1, c2) merge(c1, c2, by=by.c, all=T), cbList)

+  unionCb <- Reduce(function(c1, c2) merge(c1, c2, by=by.c, all=TRUE), cbList)

   rownames(unionCb) <- unionCb[['rownames']]

   newCbList <- list()

   for (i in seq_along(sceList)) {

@@ -234,7 +234,7 @@ combineSCE <- function(sceList, by.r, by.c, combined){

   assayList <- .mergeAssaySCE(sceList) 

   New_SCE <- list()

-  for (i in 1:length(sceList)) {

+  for (i in seq(length(sceList))) {

     ## create new sce

     New_SCE[[i]] <- .constructSCE(matrices = assayList[[i]], features = newFeList,

                                   barcodes = newCbList[[i]], 

@@ -249,4 +249,4 @@ combineSCE <- function(sceList, by.r, by.c, combined){

     return(sce)

   }

   return(New_SCE)

-}

\ No newline at end of file

+}

@@ -320,7 +320,7 @@ plotRunPerCellQCResults <- function(inSCE,

       plotlist <- c(merged.plots, list(Sample = plotlist))

     }

   } else {

-    plotlist <- unlist(plotlist, recursive=F)

+    plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

@@ -709,7 +709,7 @@ plotScrubletResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

@@ -1061,7 +1061,7 @@ plotDoubletFinderResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -1309,7 +1309,7 @@ plotDoubletCellsResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -1578,7 +1578,7 @@ plotCxdsResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -1847,7 +1847,7 @@ plotBcdsResults <- function(inSCE,

     names(plotlist) <- samples

     plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-    plotlist <- unlist(plotlist, recursive=F)

+    plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -2116,7 +2116,7 @@ plotScdsHybridResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -2382,7 +2382,7 @@ plotDecontXResults <- function(inSCE,

       names(plotlist) <- samples

       plotlist <- c(merged.plots, list(Sample = plotlist))

   } else {

-      plotlist <- unlist(plotlist, recursive=F)

+      plotlist <- unlist(plotlist, recursive=FALSE)

   }

   if(!is.null(combinePlot)){

     if(combinePlot %in% c("all", "sample")){

@@ -78,7 +78,7 @@ importMultipleSources <- function(allImportEntries) {

   return(combineSCE(sceList = sceObjs,

                     by.r = NULL,

                     by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),

-                    combined = T)

+                    combined = TRUE)

   )

 }

@@ -393,87 +393,3 @@ qcInputProcess <- function(preproc,

     stop(paste0("'", preproc, "' not supported."))

 }

-

-#' Imports samples from different sources and compiles them into a list of SCE objects

-#' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)

-#' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing

-#' the droplet or cell data or both,depending on the dataType that users provided.

-#' @export

-importMultipleSources <- function(allImportEntries) {

-  sceObjs <- list()

-  for (entry in allImportEntries$samples) {

-    if (entry$type == "cellRanger2") {

-      if (is.null(entry$params$cellRangerDirs)) {

-        newSce <- importCellRangerV2Sample(

-          dataDir = entry$params$dataDir,

-          sampleName = entry$params$sampleName,

-        )

-      } else {

-        newSce <- importCellRangerV2(

-          cellRangerDirs = entry$params$cellRangerDirs,

-          sampleDirs = entry$params$sampleDirs,

-          sampleNames = entry$params$sampleNames,

-        )

-      }

-

-    } else if (entry$type == "cellRanger3") {

-      if (is.null(entry$params$cellRangerDirs)) {

-        newSce <- importCellRangerV3Sample(

-          dataDir = entry$params$dataDir,

-          sampleName = entry$params$sampleName,

-        )

-      } else {

-        newSce <- importCellRangerV3(

-          cellRangerDirs = entry$params$cellRangerDirs,

-          sampleDirs = entry$params$sampleDirs,

-          sampleNames = entry$params$sampleNames,

-        )

-      }

-    } else if (entry$type == "starSolo") {

-      newSce <- importSTARsolo(

-        STARsoloDirs = entry$params$STARsoloDirs,

-        samples = entry$params$amples

-      )

-    } else if (entry$type == "busTools") {

-      newSce <- importBUStools(

-        BUStoolsDirs = entry$params$BUStoolsDirs,

-        samples = entry$params$samples,

-      )

-    } else if (entry$type == "seqc") {

-      newSce <- importSEQC(

-        seqcDirs = entry$params$seqcDirs,

-        samples = entry$params$samples,

-        prefix = entry$params$prefix,

-      )

-    } else if (entry$type == "optimus") {

-      newSce <- importOptimus(

-        OptimusDirs = entry$params$OptimusDirs,

-        samples = entry$params$samples

-      )

-    } else if (entry$type == "files") {

-      newSce <- importFromFiles(assayFile = entry$params$assayFile,

-                                annotFile = entry$params$annotFile,

-                                featureFile = entry$params$featureFile,

-                                assayName = entry$params$assayName)

-    } else if (entry$type == "example") {

-      newSce <- withConsoleMsgRedirect(importExampleData(dataset = entry$params$dataset))

-    } else if (entry$type == "rds") {

-      importedrds <- readRDS(entry$params$rdsFile)

-      if (base::inherits(importedrds, "SummarizedExperiment")) {

-        newSce <- importedrds

-      } else if (base::inherits(importedrds, "Seurat")) {

-        newSce <- convertSeuratToSCE(importedrds)

-      } else {

-        shiny::showNotification("The '.rds' file should contain a 'SingleCellExperiment' or 'Seurat' object.", type = "error")

-      }

-    }

-    sceObjs = c(sceObjs, list(newSce))

-  }

-

-  return(combineSCE(sceList = sceObjs,

-                    by.r = NULL,

-                    by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),

-                    combined = T)

-         )

-}

-

@@ -67,11 +67,11 @@ subTitle <- params$subTitle

 studyDesign <- params$studyDesign

 samples <- unique(colData(sce.qc)$sample)

-reduceDims<- grep('UMAP', reducedDimNames(sce.qc), value = T)

+reduceDims<- grep('UMAP', reducedDimNames(sce.qc), value = TRUE)

 if (length(reduceDims) != 0) {

   reduceDimUsed <- reduceDims[1]

 } else {

-  reduceDims<- grep('TSNE', reducedDimNames(sce.qc), value = T)

+  reduceDims<- grep('TSNE', reducedDimNames(sce.qc), value = TRUE)

   if (length(reduceDims) == 0) {

     stop("No reduced dimension are available for QC visualization!")

   } else {

@@ -211,9 +211,9 @@ showQCResTabs <- function(obj, algoList, statuses, plotIds) {

     algo <- algoList[[i]]

     id <- paste0(algo, "Tab")

     if (is.null(statuses[[algo]])) {

-      selectTab <- F

+      selectTab <- FALSE

       if (i == 1) {

-        selectTab <- T

+        selectTab <- TRUE

       } 

       appendTab("qcResPlotTabs", tabPanel(algo, 

                                           fluidPage(id = id, 

@@ -41,7 +41,7 @@ shinyPanelQC <- fluidPage(

                      numericInput("DXdbscanEps", "dbscanEps - Clustering resolution parameter (if no cell cluster labels) (default 1)", 1),

                      checkboxInput("DXestDelta", "estimateDelta - Estimate delta?"), # T/F input

-                     checkboxInput("DXverbose", "verbose - Print log messages?", value = T), # T/F input

+                     checkboxInput("DXverbose", "verbose - Print log messages?", value = TRUE), # T/F input

             )

           ),

           tags$hr(),

@@ -67,7 +67,7 @@ shinyPanelQC <- fluidPage(

                      numericInput("CXntop", "ntop - Number of top variance genes (default 500)", 500),

                      numericInput("CXbinThresh", "binThresh - Threshold to consider a gene 'present' (default 0)", 0),

-                     checkboxInput("CXverb", "verb - Output progress messages?", value = T), # T/F input

+                     checkboxInput("CXverb", "verb - Output progress messages?", value = TRUE), # T/F input

                      checkboxInput("CXretRes", "retRes - Return gene pair scores and top-scoring gene pairs?"), # T/F input

                      checkboxInput("CXestNdbl", "estNdbl - Estimate the number of doublets?"), # T/F input

             )

@@ -84,7 +84,7 @@ shinyPanelQC <- fluidPage(

                      textInput("BCnmax", "nmax - Max number of training rounds (default 'tune')", value = "tune"),

-                     checkboxInput("BCverb", "verb - Output progress messages?", value = T), # T/F input

+                     checkboxInput("BCverb", "verb - Output progress messages?", value = TRUE), # T/F input

                      checkboxInput("BCretRes", "retRes - Return trained classifier?"), # T/F input

                      checkboxInput("BCvarImp", "varImp - Return variable importance?"), # T/F input

                      checkboxInput("BCestNdbl", "estNdbl - Estimate the number of doublets?"), # T/F input

@@ -110,8 +110,8 @@ shinyPanelQC <- fluidPage(

                      checkboxInput("BC2retRes", "retRes - Return trained classifier?"), # T/F input

                      checkboxInput("BC2varImp", "varImp - Return variable importance?"), # T/F input

-                     checkboxInput("CXBCverb", "verb - Output bcds progress messages?", value = T), # T/F input

-                     checkboxInput("CXBCestNdbl", "estNdbl - Estimate the number of doublets?", value = T), # T/F input

+                     checkboxInput("CXBCverb", "verb - Output bcds progress messages?", value = TRUE), # T/F input

+                     checkboxInput("CXBCestNdbl", "estNdbl - Estimate the number of doublets?", value = TRUE), # T/F input

             )

           ),

           # scrublet

@@ -136,12 +136,12 @@ shinyPanelQC <- fluidPage(

                      textInput("SdistanceMetric", "distanceMetric - Distance metric", value = "euclidean"),

-                     checkboxInput("SuseApproxNeighbors", "useApproxNeighbors - Use approximate nearest neighbor method?", value = T), # T/F input

+                     checkboxInput("SuseApproxNeighbors", "useApproxNeighbors - Use approximate nearest neighbor method?", value = TRUE), # T/F input

                      checkboxInput("SgetDoubletNeighborParents", "getDoubletNeighborParents - Return doublet neighbors' parent transcriptomes?"), # T/F input

                      checkboxInput("SlogTransform", "logTransform - Log transform counts matrix?"), # T/F input

-                     checkboxInput("SmeanCenter", "meanCenter - Center each gene's data at zero?", value = T), # T/F input

-                     checkboxInput("SnormalizeVariance", "normalizeVariance - Normalize each gene's data to have a variance of 1?", value = T), # T/F input

-                     checkboxInput("Sverbose", "verbose - Output progress updates?", value = T), # T/F input

+                     checkboxInput("SmeanCenter", "meanCenter - Center each gene's data at zero?", value = TRUE), # T/F input

+                     checkboxInput("SnormalizeVariance", "normalizeVariance - Normalize each gene's data to have a variance of 1?", value = TRUE), # T/F input

+                     checkboxInput("Sverbose", "verbose - Output progress updates?", value = TRUE), # T/F input

             )

           ),

           # doubletFinder

@@ -156,7 +156,7 @@ shinyPanelQC <- fluidPage(

                      numericInput("DFformationRate", "formationRate - Doublet formation rate (default 0.075)", 0.075),

                      numericInput("DFseuratPcs", "seuratPcs - PCs to determine the number of clusters (default 15)", 15),

-                     checkboxInput("DFverbose", "verbose - Output log messages?", value = T), # T/F input

+                     checkboxInput("DFverbose", "verbose - Output log messages?", value = TRUE), # T/F input

             )

           ),

           tags$hr(),