@@ -165,9 +165,9 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") {

     new.clusters <- plyr::mapvalues(celdaClusters(sce,

                                                   altExpName = altExpName),

                                     from, to)

-    new.clusters <- factor(new.clusters, levels = 

+    new.clusters <- factor(new.clusters, levels =

                              sort(as.numeric(unique(new.clusters))))

-    

+

     celdaClusters(sce, altExpName = altExpName) <- new.clusters

     return(sce)

 }

@@ -218,9 +218,9 @@ recodeClusterY <- function(sce, from, to, altExpName = "featureSubset") {

     new.clusters <- plyr::mapvalues(celdaModules(sce,

                                                   altExpName = altExpName),

                                   from, to)

-    new.clusters <- factor(new.clusters, levels = 

+    new.clusters <- factor(new.clusters, levels =

                              sort(as.numeric(unique(new.clusters))))

-  

+

     celdaModules(sce, altExpName = altExpName) <- plyr::mapvalues(

         celdaModules(sce, altExpName = altExpName), from, to)

     return(sce)

@@ -27,13 +27,13 @@

 #' @param background A numeric matrix of counts or a

 #' \linkS4class{SingleCellExperiment} with the matrix located in the assay

 #' slot under \code{assayName}. It should have the same data format as \code{x}

-#' except it contains the empty droplets instead of cells. When supplied, 

+#' except it contains the empty droplets instead of cells. When supplied,

 #' empirical distribution of transcripts from these empty droplets

 #' will be used as the contamination distribution. Default NULL.

 #' @param bgAssayName Character. Name of the assay to use if \code{background}

 #' is a \linkS4class{SingleCellExperiment}. Default to same as

 #' \code{assayName}.

-#' @param bgBatch Numeric or character vector. Batch labels for 

+#' @param bgBatch Numeric or character vector. Batch labels for

 #' \code{background}. Its unique values should be the same as those in

 #' \code{batch}, such that each batch of cells have their corresponding batch

 #' of empty droplets as background, pointed by this parameter. Default to NULL.

@@ -174,10 +174,10 @@ setMethod("decontX", "SingleCellExperiment", function(x,

                              bgBatch = bgBatch,

                              logfile = logfile,

                              verbose = verbose)

-    

+

     background <- temp$background

     bgBatch <- temp$bgBatch

-    

+

     if (is.null(bgAssayName)) {

       bgAssayName <- assayName

     }

@@ -265,10 +265,10 @@ setMethod("decontX", "ANY", function(x,

                              bgBatch = bgBatch,

                              logfile = logfile,

                              verbose = verbose)

-    

+

     background <- temp$background

     bgBatch <- temp$bgBatch

-    

+

   }

   .decontX(

@@ -420,9 +420,9 @@ setMethod(

   ## Generate batch labels if none were supplied

   if (is.null(batch)) {

     batch <- rep("all_cells", nC)

-    

+

     # If batch null, bgBatch has to be null

-    if (!is.null(batchBackground)){

+    if (!is.null(batchBackground)) {

       stop(

         "When experiment default to no bacth, background should ",

         "also default to no batch."

@@ -436,7 +436,7 @@ setMethod(

     # If batch not null and countsBackground supplied,

     # user has to supply batchBackground as well

-    if (!is.null(countsBackground) & is.null(batchBackground)){

+    if (!is.null(countsBackground) & is.null(batchBackground)) {

       stop(

         "Cell batch, and background are supplied. Please also ",

         "supply background batch."

@@ -540,7 +540,7 @@ setMethod(

     }

     ## Try to convert class of new matrix to class of original matrix

-    

+

     .logMessages(

       date(),

       ".. Calculating final decontaminated matrix",

@@ -612,7 +612,7 @@ setMethod(

       append = TRUE,

       verbose = verbose

     )

-    

+

     ## Determine class of seed in DelayedArray

     seed.class <- unique(DelayedArray::seedApply(counts, class))[[1]]

     if (seed.class == "HDF5ArraySeed") {

@@ -1422,7 +1422,7 @@ simulateContamination <- function(C = 300,

                              logfile = NULL, verbose = FALSE) {

   # Remove background barcodes that have already appeared in x

   # If bgBatch param is supplied, also remove duplicate bgBatch

-  if(!is.null(colnames(background))) {

+  if (!is.null(colnames(background))) {

     dupBarcode <- colnames(background) %in% colnames(x)

   } else {

     dupBarcode <- FALSE

@@ -1432,7 +1432,7 @@ simulateContamination <- function(C = 300,

             " Please ensure that no true cells are included in the background ",

             "matrix. Otherwise, results will be incorrect.")

   }

-  

+

   if (any(dupBarcode)) {

     .logMessages(

       date(),

@@ -1445,8 +1445,8 @@ simulateContamination <- function(C = 300,

       verbose = verbose

     )

     background <- background[, !(dupBarcode), drop = FALSE]

-    

-    if(!is.null(bgBatch)){

+

+    if (!is.null(bgBatch)) {

       if (length(bgBatch) != length(dupBarcode)) {

         stop(

           "Length of bgBatch must be equal to the number of columns",

@@ -1456,9 +1456,9 @@ simulateContamination <- function(C = 300,

       bgBatch <- bgBatch[!(dupBarcode)]

     }

   }

-  

-  re = list(background = background,

+

+  re <- list(background = background,

             bgBatch = bgBatch)

-  

+

   return(re)

 }