@@ -70,30 +70,36 @@

 }

-.mergeRowDataSCE <- function(sceList, by.r) {

-  feList <- lapply(sceList, function(x){

-    rw <- SummarizedExperiment::rowData(x)

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

-    return(rw)

-  })

-  

-  ## Get merged rowData

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

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

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

-  

-  ## rowData

-  newFe <- unionFe

-  if (nrow(newFe) != length(allGenes)) {

-    warning("Conflicts were found when merging two rowData. ",

-            "Resolved the conflicts by choosing the first entries.",

-            "To avoid conflicts, please provide the 'by.r' arguments to ",

-            "specify columns in rowData that does not have conflict between two singleCellExperiment object. ")

-    newFe <- newFe[!duplicated(newFe$rownames), ]

-  }

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

-  newFe <- newFe[allGenes,]

-  return(newFe)

+.mergeRowDataSCE <- function(sce.list, by.r) {

+    feList <- lapply(sce.list, function(x){

+        rw <- SummarizedExperiment::rowData(x)

+        rw[['rownames']] <- rownames(rw)

+        return(rw)

+    })

+    

+    ## Get merged rowData

+    if (is.null(by.r)) {

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

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

+    }

+    else {

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

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

+    }

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

+    

+    ## rowData

+    newFe <- unionFe

+    if (nrow(newFe) != length(allGenes)) {

+        warning("Conflicts were found when merging two rowData. ",

+                "Resolved the conflicts by choosing the first entries.",

+                "To avoid conflicts, please provide the 'by.r' arguments to ",

+                "specify columns in rowData that does not have conflict between two singleCellExperiment object. ")

+        newFe <- newFe[!duplicated(newFe$rownames), ]

+    }

+    rownames(newFe) <- newFe[['rownames']]

+    newFe <- newFe[allGenes,]

+    return(newFe)

 }

 .mergeColDataSCE <- function(sceList, by.c) {

@@ -103,8 +109,15 @@

     return(cD)

   })

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

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

+  # Merge columns

+  if (is.null(by.c)) {

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

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

+  }

+  else {

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

+    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)) {

@@ -1,4 +1,4 @@

-#' @title Perform comprehensive single cell QC

+#' @title Single Cell QC checking

 #' @description Utility functions for runQC - checking cell input for validity

 #' @param FilterFile The cell QC object as rendered in R

 #' @param FilterDir The cell QC file location

@@ -50,7 +50,7 @@

     return(0)

 }

-#' @title Perform comprehensive single cell QC

+#' @title Single Cell QC checking

 #' @description Utility functions for runQC - checking droplet input for validity

 #' @param RawFile The droplet QC object as rendered in R

 #' @param RawDir The droplet QC file location

@@ -101,7 +101,7 @@

     return(0)

 }

-#' @title Perform comprehensive single cell QC

+#' @title Single Cell QC checking

 #' @description Utility functions for runQC - checking cell and droplet input for validity

 #' @param RawFile The droplet QC object as rendered in R

 #' @param RawDir The droplet QC file location

@@ -174,6 +174,7 @@

 #' @description QC execution function wrapper for cell SCE objects

 #' @param cellSCE The cell SCE object as rendered in R

 #' @param preproc The method that we are looking at, be it CellRanger, Seurat, SCE, AnnData, or otherwise. 

+#' @param geneSetCollection Reference library of genes

 #' @param Params The list of parameters we are using.

 #' @param cellQCAlgos The list of various QC algorithms to use.

 #' @param mitoInfo Reference library for MitoGenes

@@ -35,9 +35,7 @@

         AnnData$var_names <- rownames(SCE)

     }

     # uns  <- S4Vectors::metadata(SCE)

-    # if(length(uns) > 0){

-    #     AnnData$uns <- uns

-    # }

+    # if(length(uns) > 0){ AnnData$uns <- uns }

     obsmNames <- SingleCellExperiment::reducedDimNames(SCE)

     if(length(obsmNames) > 0){

         for (i in seq_along(obsmNames)) {

@@ -51,10 +49,7 @@

     for (i in seq_along(allAssayNames)) {

         oneName <- allAssayNames[i]

         if (!oneName == useAssay) {

-            AnnData$layers$'__setitem__'(oneName,

-                                         as.matrix(

-                                             t(SummarizedExperiment::assay(

-                                                 SCE, oneName))))

+            AnnData$layers$'__setitem__'(oneName, as.matrix(t(SummarizedExperiment::assay(SCE, oneName))))

         }

     }

     return(AnnData)

new file mode 100644

@@ -0,0 +1,37 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runQCUtils.R

+\name{.checkBoth}

+\alias{.checkBoth}

+\title{Perform comprehensive single cell QC}

+\usage{

+.checkBoth(

+  RawFile,

+  FilterFile,

+  RawDir,

+  FilterDir,

+  basepath,

+  Reference,

+  process

+)

+}

+\arguments{

+\item{RawFile}{The droplet QC object as rendered in R}

+

+\item{FilterFile}{The cell QC object as rendered in R}

+

+\item{RawDir}{The droplet QC file location}

+

+\item{FilterDir}{The cell QC file location}

+

+\item{basepath}{The base/root directory of the QC files.}

+

+\item{Reference}{Reference library for MitoGenes}

+

+\item{process}{The method that we are looking at, be it CellRanger, Seurat, SCE, AnnData, or otherwise.}

+}

+\value{

+0 if the check is completed successfully, else a premature stop.

+}

+\description{

+Utility functions for runQC - checking cell and droplet input for validity

+}

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runQCUtils.R

+\name{.checkCell}

+\alias{.checkCell}

+\title{Perform comprehensive single cell QC}

+\usage{

+.checkCell(FilterFile, FilterDir, basepath, Reference, process)

+}

+\arguments{

+\item{FilterFile}{The cell QC object as rendered in R}

+

+\item{FilterDir}{The cell QC file location}

+

+\item{basepath}{The base/root directory of the QC files.}

+

+\item{Reference}{Reference library for MitoGenes}

+

+\item{process}{The method that we are looking at, be it CellRanger, Seurat, SCE, AnnData, or otherwise.}

+}

+\value{

+0 if the check is completed successfully, else a premature stop.

+}

+\description{

+Utility functions for runQC - checking cell input for validity

+}

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runQCUtils.R

+\name{.checkDroplet}

+\alias{.checkDroplet}

+\title{Perform comprehensive single cell QC}

+\usage{

+.checkDroplet(RawFile, RawDir, basepath, Reference, process)

+}

+\arguments{

+\item{RawFile}{The droplet QC object as rendered in R}

+

+\item{RawDir}{The droplet QC file location}

+

+\item{basepath}{The base/root directory of the QC files.}

+

+\item{Reference}{Reference library for MitoGenes}

+

+\item{process}{The method that we are looking at, be it CellRanger, Seurat, SCE, AnnData, or otherwise.}

+}

+\value{

+0 if the check is completed successfully, else a premature stop.

+}

+\description{

+Utility functions for runQC - checking droplet input for validity

+}

new file mode 100644

@@ -0,0 +1,27 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runQCUtils.R

+\name{.runCell}

+\alias{.runCell}

+\title{Perform comprehensive single cell QC}

+\usage{

+.runCell(cellSCE, preproc, geneSetCollection, Params, cellQCAlgos, mitoInfo)

+}

+\arguments{

+\item{cellSCE}{The cell SCE object as rendered in R}

+

+\item{preproc}{The method that we are looking at, be it CellRanger, Seurat, SCE, AnnData, or otherwise.}

+

+\item{geneSetCollection}{Reference library of genes}

+

+\item{Params}{The list of parameters we are using.}

+

+\item{cellQCAlgos}{The list of various QC algorithms to use.}

+

+\item{mitoInfo}{Reference library for MitoGenes}

+}

+\value{

+No objects are returned, just runs the cell QC and throws an error if problems occur in subfunctions

+}

+\description{

+QC execution function wrapper for cell SCE objects

+}

new file mode 100644

@@ -0,0 +1,37 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/runQCUtils.R

+\name{.runDroplet}

+\alias{.runDroplet}

+\title{Perform comprehensive single cell QC}

+\usage{

+.runDroplet(

+  dropletSCE,

+  geneSetCollection,

+  Params,

+  mitoInfo,

+  cellQCAlgos,

+  detectCell,

+  cellCalling

+)

+}

+\arguments{

+\item{dropletSCE}{The cell SCE object as rendered in R}

+

+\item{geneSetCollection}{Reference library of genes}

+

+\item{Params}{The list of parameters we are using.}

+

+\item{mitoInfo}{Reference library for MitoGenes}

+

+\item{cellQCAlgos}{The list of various QC algorithms to use.}

+

+\item{detectCell}{Whether or not to detect the cell SCE object, or not}

+

+\item{cellCalling}{The cell algorithm to be used.}

+}

+\value{

+No objects are returned, just runs the cell QC and throws an error if problems occur in subfunctions

+}

+\description{

+QC execution function wrapper for droplet SCE objects

+}

@@ -6,7 +6,8 @@

 \usage{

 getSceParams(

   inSCE,

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

+  skip = c("runScrublet", "runDecontX", "runBarcodeRanksMetaOutput", "genesets",

+    "runSoupX"),

   ignore = c("algorithms", "estimates", "contamination", "z", "sample", "rank",

     "BPPARAM", "batch", "geneSetCollection", "barcodeArgs"),

   directory = "./",

Binary files a/tests/testthat/Rplots.pdf and b/tests/testthat/Rplots.pdf differ