@@ -64,6 +64,7 @@ export(retrieveFeatureIndex)

 export(runParams)

 export(sampleLabel)

 export(selectBestModel)

+export(selectFeatures)

 export(simulateCells)

 export(simulateContamination)

 export(splitModule)

@@ -116,6 +117,7 @@ exportMethods(resamplePerplexity)

 exportMethods(runParams)

 exportMethods(sampleLabel)

 exportMethods(selectBestModel)

+exportMethods(selectFeatures)

 exportMethods(splitModule)

 exportMethods(subsetCeldaList)

 import(Rcpp)

@@ -1,5 +1,5 @@

 #' @title Get or set the cell cluster labels from a celda

-#'  \linkS4class{SingleCellExperiment}  object or celda model

+#'  \linkS4class{SingleCellExperiment} object or celda model

 #'  object.

 #' @description Return or set the cell cluster labels determined

 #'  by \link{celda_C} or \link{celda_CG} models.

@@ -7,9 +7,12 @@

 #'  \itemize{

 #'  \item A \linkS4class{SingleCellExperiment} object returned by

 #'  \link{celda_C}, or \link{celda_CG}, with the matrix

-#'  located in the \code{useAssay} assay slot.

-#'  Rows represent features and columns represent cells.

+#'  located in the \code{useAssay} assay slot. The

+#'  a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will

+#'  be used. Rows represent features and columns represent cells.

 #'  \item Celda model object.}

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param value Character vector of cell cluster labels for replacements. Works

 #'  only if \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @return One of

@@ -22,7 +25,7 @@

 #'  Models) and/or feature module labels (for celda_G and celdaCG Models).}

 #' @export

 setGeneric("celdaClusters",

-    function(x) {

+    function(x, ...) {

         standardGeneric("celdaClusters")

     })

@@ -34,8 +37,9 @@ setGeneric("celdaClusters",

 #' @export

 setMethod("celdaClusters",

     signature(x = "SingleCellExperiment"),

-    function(x) {

-        return(SummarizedExperiment::colData(x)$celda_cell_cluster)

+    function(x, altExpName = "featureSubset") {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        return(SummarizedExperiment::colData(altExp)$celda_cell_cluster)

     })

@@ -55,34 +59,38 @@ setMethod("celdaClusters",

 #' @rdname celdaClusters

 #' @export

 setGeneric("celdaClusters<-",

-    function(x, value) standardGeneric("celdaClusters<-")

+    function(x, ...) standardGeneric("celdaClusters<-")

 )

 #' @rdname celdaClusters

 #' @export

 setReplaceMethod("celdaClusters", signature(x = "SingleCellExperiment"),

-    function(x, value) {

-        SummarizedExperiment::colData(x)$celda_cell_cluster <- value

+    function(x, altExpName = "featureSubset", value) {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        SummarizedExperiment::colData(altExp)$celda_cell_cluster <- value

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

         return(x)

     })

 #' @title Get or set the feature module labels from a celda

-#'  \linkS4class{SingleCellExperiment}  object.

+#'  \linkS4class{SingleCellExperiment} object.

 #' @description Return or set the feature module cluster labels determined

 #'  by \link{celda_G} or \link{celda_CG} models.

 #' @param sce A \linkS4class{SingleCellExperiment} object returned by

 #'  \link{celda_G}, or \link{celda_CG}, with the matrix

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param value Character vector of feature module labels for replacements.

 #'  Works only if \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @return Character vector. Contains feature module labels for each

 #'  feature in x.

 #' @export

 setGeneric("celdaModules",

-    function(sce) {

+    function(sce, ...) {

         standardGeneric("celdaModules")

     })

@@ -94,23 +102,26 @@ setGeneric("celdaModules",

 #' @export

 setMethod("celdaModules",

     signature(sce = "SingleCellExperiment"),

-    function(sce) {

-        return(SummarizedExperiment::rowData(sce)$celda_feature_module)

+    function(sce, altExpName = "featureSubset") {

+        altExp <- SingleCellExperiment::altExp(sce, altExpName)

+        return(SummarizedExperiment::rowData(altExp)$celda_feature_module)

     })

 #' @rdname celdaModules

 #' @export

 setGeneric("celdaModules<-",

-    function(sce, value) standardGeneric("celdaModules<-")

+    function(sce, ...) standardGeneric("celdaModules<-")

 )

 #' @rdname celdaModules

 #' @export

 setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"),

-    function(sce, value) {

+    function(sce, altExpName = "featureSubset", value) {

+        altExp <- SingleCellExperiment::altExp(sce, altExpName)

         SummarizedExperiment::rowData(sce)$celda_feature_module <- value

+        SingleCellExperiment::altExp(sce, altExpName) <- altExp

         return(sce)

     })

@@ -125,13 +136,15 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"),

 #'  located in the \code{useAssay} assay slot.

 #'  Rows represent features and columns represent cells.

 #'  \item A celda model object.}

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param value Character vector of sample labels for replacements. Works

 #'  only is \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @return Character vector. Contains the sample labels provided at model

 #'  creation, or those automatically generated by celda.

 #' @export

 setGeneric("sampleLabel",

-    function(x) {

+    function(x, ...) {

         standardGeneric("sampleLabel")

     })

@@ -143,21 +156,24 @@ setGeneric("sampleLabel",

 #' @export

 setMethod("sampleLabel",

     signature(x = "SingleCellExperiment"),

-    function(x) {

-        return(SummarizedExperiment::colData(x)$celda_sample_label)

+    function(x, altExpName = "featureSubset") {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        return(SummarizedExperiment::colData(altExp)$celda_sample_label)

     })

 #' @rdname sampleLabel

 #' @export

 setGeneric("sampleLabel<-",

-    function(x, value) standardGeneric("sampleLabel<-")

+    function(x, ...) standardGeneric("sampleLabel<-")

 )

 #' @rdname sampleLabel

 #' @export

 setReplaceMethod("sampleLabel", signature(x = "SingleCellExperiment"),

-    function(x, value) {

-        SummarizedExperiment::colData(x)$celda_sample_label <- value

+    function(x, altExpName = "featureSubset", value) {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        SummarizedExperiment::colData(altExp)$celda_sample_label <- value

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

         return(x)

     })

@@ -238,13 +254,14 @@ setMethod("matrixNames",

 #'  priors from the celdaList object when it was created.

 #' @param x An object of class \linkS4class{SingleCellExperiment} or class

 #'  \code{celdaList}.

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @return Data Frame. Contains details on the various K/L parameters, chain

 #'  parameters, seed, and final log-likelihoods derived for each model in the

 #'  provided celdaList.

 #' @export

-setGeneric(

-    "runParams",

-    function(x) {

+setGeneric("runParams",

+    function(x, ...) {

         standardGeneric("runParams")

     }

 )

@@ -257,8 +274,9 @@ setGeneric(

 #' @export

 setMethod("runParams",

     signature(x = "SingleCellExperiment"),

-    function(x) {

-        return(x@metadata$celda_grid_search@runParams)

+    function(x, altExpName = "featureSubset") {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        return(altExp@metadata$celda_grid_search@runParams)

     }

 )

@@ -282,12 +300,14 @@ setMethod("runParams",

 #'  \link{celdaGridSearch} run.

 #' @param x An object of class \linkS4class{SingleCellExperiment} or

 #'  \code{celdaList}.

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @return List. Contains one celdaModel object for each of the parameters

 #'  specified in \code{runParams(x)}.

 #' @export

 setGeneric(

     "resList",

-    function(x) {

+    function(x, ...) {

         standardGeneric("resList")

     }

 )

@@ -300,8 +320,9 @@ setGeneric(

 #' @export

 setMethod("resList",

     signature(x = "SingleCellExperiment"),

-    function(x) {

-        return(x@metadata$celda_grid_search@resList)

+    function(x, altExpName = "featureSubset") {

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+        return(altExp@metadata$celda_grid_search@resList)

     }

 )

@@ -317,3 +338,121 @@ setMethod("resList",

         return(x@resList)

     }

 )

+

+

+#' @title Get celda model from a celda

+#'  \link[SingleCellExperiment]{SingleCellExperiment} object

+#' @description Return the celda model for \code{sce} returned by

+#'  \link{celda_C}, \link{celda_G} or \link{celda_CG}.

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

+#'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

+#' @return Character. The celda model. Can be one of "celda_C", "celda_G", or

+#'  "celda_CG".

+#' @examples

+#' data(sceCeldaCG)

+#' celdaModel(sceCeldaCG)

+#' @export

+setGeneric("celdaModel",

+    function(sce, ...) {

+        standardGeneric("celdaModel")

+    })

+#' @rdname celdaModel

+#' @export

+setMethod("celdaModel",

+    signature(sce = "SingleCellExperiment"),

+    function(sce, altExpName = "featureSubset") {

+

+        if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {

+            stop(altExpName, " not in 'altExpNames(x)'. Run ",

+                "selectFeatures(x) first!")

+        }

+

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+

+        tryCatch(

+            if (S4Vectors::metadata(altExp)$celda_parameters$model %in%

+                    c("celda_C", "celda_G", "celda_CG")) {

+                return(S4Vectors::metadata(altExp)$celda_parameters$model)

+            } else {

+                stop("S4Vectors::metadata(altExp(sce,",

+                    " altExpName))$celda_parameters$model must be",

+                    " one of 'celda_C', 'celda_G', or 'celda_CG'")

+            },

+            error = function(e) {

+                message("S4Vectors::metadata(altExp(sce,",

+                    " altExpName))$celda_parameters$model must",

+                    " exist! Try running celda model (celda_C, celda_CG, or",

+                    " celda_G) first.")

+                stop(e)

+            })

+    })

+

+

+#' @title Get perplexity for every model in a celdaList

+#' @description Returns perplexity for each model in a celdaList as calculated

+#'  by `perplexity().`

+#' @param celdaList An object of class celdaList.

+#' @return List. Contains one celdaModel object for each of the parameters

+#'  specified in the `runParams()` of the provided celda list.

+#' @examples

+#' data(celdaCGGridSearchRes)

+#' celdaCGGridModelPerplexities <- celdaPerplexity(celdaCGGridSearchRes)

+#' @export

+setGeneric(

+    "celdaPerplexity",

+    function(celdaList) {

+        standardGeneric("celdaPerplexity")

+    }

+)

+#' @title Get perplexity for every model in a celdaList

+#' @description Returns perplexity for each model in a celdaList as calculated

+#'  by `perplexity().`

+#' @param celdaList An object of class celdaList.

+#' @return List. Contains one celdaModel object for each of the parameters

+#'  specified in the `runParams()` of the provided celda list.

+#' @examples

+#' data(celdaCGGridSearchRes)

+#' celdaCGGridModelPerplexities <- celdaPerplexity(celdaCGGridSearchRes)

+#' @export

+setMethod("celdaPerplexity",

+    signature = c(celdaList = "celdaList"),

+    function(celdaList) {

+        celdaList@perplexity

+    }

+)

+

+

+#' @title Get the MD5 hash of the count matrix from the celdaList

+#' @description Returns the MD5 hash of the count matrix used to generate the

+#'  celdaList.

+#' @param celdaList An object of class celdaList.

+#' @return A character string of length 32 containing the MD5 digest of

+#'  the count matrix.

+#' @examples

+#' data(celdaCGGridSearchRes)

+#' countChecksum <- countChecksum(celdaCGGridSearchRes)

+#' @export

+setGeneric(

+    "countChecksum",

+    function(celdaList) {

+        standardGeneric("countChecksum")

+    }

+)

+#' @title Get the MD5 hash of the count matrix from the celdaList

+#' @description Returns the MD5 hash of the count matrix used to generate the

+#'  celdaList.

+#' @param celdaList An object of class celdaList.

+#' @return A character string of length 32 containing the MD5 digest of

+#'  the count matrix.

+#' @examples

+#' data(celdaCGGridSearchRes)

+#' countChecksum <- countChecksum(celdaCGGridSearchRes)

+#' @export

+setMethod("countChecksum",

+    signature = c(celdaList = "celdaList"),

+    function(celdaList) {

+        celdaList@countChecksum

+    }

+)

@@ -6,14 +6,15 @@

 #'  Fixed parameters to be used in all models, such as \code{sampleLabel}, can

 #'  be passed as a list to the argument \code{paramsFixed}. When

 #'  \code{verbose = TRUE}, output from each chain will be sent to a log file

-#'  but not be displayed in stdout.

+#'  but not be displayed in \code{stdout}.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

-#'  slot to use if \code{x} is a

-#'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".

+#' @param useAssay A string specifying the name of the

+#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param model Celda model. Options available in \link{availableModels}.

 #' @param paramsTest List. A list denoting the combinations of parameters to

 #'  run in a celda model. For example,

@@ -76,6 +77,7 @@ setMethod("celdaGridSearch",

     signature(x = "SingleCellExperiment"),

     function(x,

         useAssay = "counts",

+        altExpName = "featureSubset",

         model,

         paramsTest,

         paramsFixed = NULL,

@@ -89,7 +91,19 @@ setMethod("celdaGridSearch",

         logfilePrefix = "Celda") {

         xClass <- "SingleCellExperiment"

-        counts <- SummarizedExperiment::assay(x, i = useAssay)

+

+        if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {

+            stop(altExpName, " not in 'altExpNames(x)'. Run ",

+                "selectFeatures(x) first!")

+        }

+

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+

+        if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {

+            stop(useAssay, " not in assayNames(altExp(x, altExpName))")

+        }

+

+        counts <- SummarizedExperiment::assay(altExp, i = useAssay)

         celdaList <- .celdaGridSearch(counts = counts,

             model = paste0(".", model),

@@ -104,8 +118,8 @@ setMethod("celdaGridSearch",

             verbose = verbose,

             logfilePrefix = logfilePrefix)

-        sce <- .createSCEceldaGridSearch(celdaList = celdaList,

-            sce = x,

+        altExp <- .createSCEceldaGridSearch(celdaList = celdaList,

+            sce = altExp,

             xClass = xClass,

             useAssay = useAssay,

             model = model,

@@ -119,6 +133,7 @@ setMethod("celdaGridSearch",

             perplexity = perplexity,

             verbose = verbose,

             logfilePrefix = logfilePrefix)

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

         return(sce)

     })

@@ -128,6 +143,8 @@ setMethod("celdaGridSearch",

 setMethod("celdaGridSearch",

     signature(x = "matrix"),

     function(x,

+        useAssay = "counts",

+        altExpName = "featureSubset",

         model,

         paramsTest,

         paramsFixed = NULL,

@@ -140,10 +157,12 @@ setMethod("celdaGridSearch",

         verbose = TRUE,

         logfilePrefix = "Celda") {

+        ls <- list()

+        ls[[useAssay]] <- x

+        sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)

+        SingleCellExperiment::altExp(sce, altExpName) <- sce

         xClass <- "matrix"

-        useAssay <- NULL

-        sce <- SingleCellExperiment::SingleCellExperiment(

-            assays = list(counts = x))

+

         celdaList <- .celdaGridSearch(counts = x,

             model = paste0(".", model),

             paramsTest = paramsTest,

@@ -157,8 +176,8 @@ setMethod("celdaGridSearch",

             verbose = verbose,

             logfilePrefix = logfilePrefix)

-        sce <- .createSCEceldaGridSearch(celdaList = celdaList,

-            sce = sce,

+        altExp <- .createSCEceldaGridSearch(celdaList = celdaList,

+            sce = SingleCellExperiment::altExp(sce, altExpName),

             xClass = xClass,

             useAssay = useAssay,

             model = model,

@@ -172,6 +191,7 @@ setMethod("celdaGridSearch",

             perplexity = perplexity,

             verbose = verbose,

             logfilePrefix = logfilePrefix)

+        SingleCellExperiment::altExp(sce, altExpName) <- altExp

         return(sce)

     })

@@ -422,6 +442,8 @@ setMethod("celdaGridSearch",

 #' @param useAssay A string specifying which \code{assay}

 #'  slot to use if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @return One of

 #' \itemize{

 #'  \item A new \linkS4class{SingleCellExperiment} object containing

@@ -455,13 +477,13 @@ setGeneric("subsetCeldaList", function(x, ...) {

 #' @export

 setMethod("subsetCeldaList",

     signature(x = "SingleCellExperiment"),

-    function(x, params, useAssay = "counts") {

+    function(x, params, useAssay = "counts", altExpName = "featureSubset") {

         ## Check for bad parameter names

         if (!all(names(params) %in% colnames(runParams(x)))) {

             badParams <- setdiff(names(params), colnames(runParams(x)))

             stop("The following elements in 'params' are not columns in",

-                " runParams (x) ",

+                " runParams(x) ",

                 paste(badParams, collapse = ",")

             )

         }

@@ -481,13 +503,17 @@ setMethod("subsetCeldaList",

         ## Get index of selected models, subset celdaList, and return

         ix <- match(newRunParams$index, runParams(x)$index)

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+

         if (length(ix) == 1) {

-            x <- .subsetCeldaListSCE(x, ix)

+            altExp <- .subsetCeldaListSCE(altExp, ix)

         } else {

-            x@metadata$celda_grid_search@runParams <-

+            altExp@metadata$celda_grid_search@runParams <-

                 as.data.frame(newRunParams)

-            x@metadata$celda_grid_search@resList <- resList(x)[ix]

+            altExp@metadata$celda_grid_search@resList <-

+                altExp@metadata$celda_grid_search@resList[ix]

         }

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

         return(x)

     }

 )

@@ -555,6 +581,8 @@ setMethod("subsetCeldaList",

 #' @param useAssay A string specifying which \code{assay}

 #'  slot to use if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @return One of

 #' \itemize{

 #'  \item A new \linkS4class{SingleCellExperiment} object containing

@@ -585,11 +613,14 @@ setGeneric("selectBestModel", function(x, ...) {

 #' @importFrom data.table as.data.table

 #' @export

 setMethod("selectBestModel", signature(x = "SingleCellExperiment"),

-    function(x, asList = FALSE, useAssay = "counts") {

+    function(x, asList = FALSE, useAssay = "counts",

+        altExpName = "featureSubset") {

+

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

         logLikelihood <- NULL

         group <- setdiff(colnames(runParams(x)),

             c("index", "chain", "logLikelihood", "mean_perplexity", "seed"))

-        runParams <- S4Vectors::metadata(x)$celda_grid_search@runParams

+        runParams <- S4Vectors::metadata(altExp)$celda_grid_search@runParams

         dt <- data.table::as.data.table(runParams)

         newRunParams <- as.data.frame(dt[, .SD[which.max(logLikelihood)],

             by = group])

@@ -597,12 +628,14 @@ setMethod("selectBestModel", signature(x = "SingleCellExperiment"),

         ix <- match(newRunParams$index, runParams$index)

         if (nrow(newRunParams) == 1 & !asList) {

-            x <- .subsetCeldaListSCE(x, ix)

+            altExp <- .subsetCeldaListSCE(altExp, ix)

         } else {

-            x@metadata$celda_grid_search@runParams <-

+            altExp@metadata$celda_grid_search@runParams <-

                 as.data.frame(newRunParams)

-            x@metadata$celda_grid_search@resList <- resList(x)[ix]

+            altExp@metadata$celda_grid_search@resList <-

+                altExp@metadata$celda_grid_search@resList[ix]

         }

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

         return(x)

     }

 )

@@ -676,7 +709,8 @@ setMethod("selectBestModel", signature(x = "celdaList"),

 .subsetCeldaListSCE <- function(x, ix) {

     cgsparam <- x@metadata$celda_grid_search@celdaGridSearchParameters

     if (cgsparam$model == "celda_C") {

-        x <- .createSCEceldaC(celdaCMod = resList(x)[[ix]],

+        x <- .createSCEceldaC(celdaCMod =

+                x@metadata$celda_grid_search@resList[[ix]],

             sce = x,

             xClass = cgsparam$xClass,

             useAssay = cgsparam$useAssay,

@@ -691,7 +725,8 @@ setMethod("selectBestModel", signature(x = "celdaList"),

             logfile = cgsparam$logfile,

             verbose = cgsparam$verbose)

     } else if (cgsparam$model == "celda_G") {

-        x <- .createSCEceldaG(celdaGMod = resList(x)[[ix]],

+        x <- .createSCEceldaG(celdaGMod =

+                x@metadata$celda_grid_search@resList[[ix]],

             sce = x,

             xClass = cgsparam$xClass,

             useAssay = cgsparam$useAssay,

@@ -705,7 +740,8 @@ setMethod("selectBestModel", signature(x = "celdaList"),

             logfile = cgsparam$logfile,

             verbose = cgsparam$verbose)

     } else if (cgsparam$model == "celda_CG") {

-        x <- .createSCEceldaCG(celdaCGMod = resList(x)[[ix]],

+        x <- .createSCEceldaCG(celdaCGMod =

+                x@metadata$celda_grid_search@resList[[ix]],

             sce = x,

             xClass = cgsparam$xClass,

             useAssay = cgsparam$useAssay,

@@ -722,7 +758,7 @@ setMethod("selectBestModel", signature(x = "celdaList"),

             logfile = cgsparam$logfile,

             verbose = cgsparam$verbose)

     } else {

-        stop("S4Vectors::metadata(X)$celda_grid_search@",

+        stop("S4Vectors::metadata(altExp(x, altExpName))$celda_grid_search@",

             "celdaGridSearchParameters$model must be",

             " one of 'celda_C', 'celda_G', or 'celda_CG'")

     }

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

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

 #' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

 #'  slot to use. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param level Character. One of "cellPopulation" or "Sample".

 #'  "cellPopulation" will display the absolute probabilities and relative

 #'  normalized expression of each module in each cell population.

@@ -33,19 +35,23 @@ setGeneric("celdaProbabilityMap",

 #' celdaProbabilityMap(sceCeldaCG)

 #' @export

 setMethod("celdaProbabilityMap", signature(sce = "SingleCellExperiment"),

-    function(sce, useAssay = "counts", level = c("cellPopulation", "sample")) {

+    function(sce, useAssay = "counts", altExpName = "featureSubset",

+        level = c("cellPopulation", "sample")) {

+

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

         level <- match.arg(level)

         if (celdaModel(sce) == "celda_C") {

             if (level == "cellPopulation") {

                 warning("'level' has been set to 'sample'")

             }

-            pm <- .celdaProbabilityMapC(sce = sce, useAssay = useAssay,

+            pm <- .celdaProbabilityMapC(sce = altExp, useAssay = useAssay,

                 level = "sample")

         } else if (celdaModel(sce) == "celda_CG") {

-            pm <- .celdaProbabilityMapCG(sce = sce, useAssay = useAssay,

+            pm <- .celdaProbabilityMapCG(sce = altExp, useAssay = useAssay,

                 level = level)

         } else {

-            stop("S4Vectors::metadata(sce)$celda_parameters$model must be",

+            stop("S4Vectors::metadata(altExp(sce,",

+                " altExpName))$celda_parameters$model must be",

                 " one of 'celda_C', or 'celda_CG'!")

         }

         return(pm)

@@ -57,10 +63,12 @@ setMethod("celdaProbabilityMap", signature(sce = "SingleCellExperiment"),

     counts <- SummarizedExperiment::assay(sce, i = useAssay)

     counts <- .processCounts(counts)

-    zInclude <- which(tabulate(celdaClusters(sce),

+    zInclude <- which(tabulate(SummarizedExperiment::colData(

+        sce)$celda_cell_cluster,

         S4Vectors::metadata(sce)$celda_parameters$K) > 0)

-    factorized <- factorizeMatrix(x = sce, useAssay = useAssay)

+    factorized <- .factorizeMatrixCelda_C(x = sce, useAssay = useAssay,

+        type = "proportion")

     samp <- factorized$proportions$sample[zInclude, , drop = FALSE]

     col <- grDevices::colorRampPalette(c("white",

@@ -108,22 +116,23 @@ setMethod("celdaProbabilityMap", signature(sce = "SingleCellExperiment"),

     counts <- SummarizedExperiment::assay(sce, i = useAssay)

     counts <- .processCounts(counts)

-    factorized <- factorizeMatrix(sce, useAssay)

-    zInclude <- which(tabulate(celdaClusters(sce),

+    factorized <- .factorizeMatrixCelda_CG(sce, useAssay,

+        type = c("counts", "proportion"))

+    zInclude <- which(tabulate(SummarizedExperiment::colData(

+        sce)$celda_cell_cluster,

         S4Vectors::metadata(sce)$celda_parameters$K) > 0)

-    yInclude <- which(tabulate(celdaModules(sce),

+    yInclude <- which(tabulate(SummarizedExperiment::rowData(

+        sce)$celda_feature_module,

         S4Vectors::metadata(sce)$celda_parameters$L) > 0)

     if (level == "cellPopulation") {

         pop <- factorized$proportions$cellPopulation[yInclude,

             zInclude,

-            drop = FALSE

-            ]

+            drop = FALSE]

         popNorm <- normalizeCounts(pop,

             normalize = "proportion",

             transformationFun = sqrt,

-            scaleFun = base::scale

-        )

+            scaleFun = base::scale)

         percentile9 <- round(stats::quantile(pop, .9), digits = 2) * 100

         col1 <- grDevices::colorRampPalette(c(

@@ -10,6 +10,8 @@

 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.

 #' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

 #'  slot to use. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param maxCells Integer. Maximum number of cells to plot. Cells will be

 #'  randomly subsampled if \code{ncol(sce) > maxCells}. Larger numbers of cells

 #'  requires more memory. If NULL, no subsampling will be performed.

@@ -76,6 +78,7 @@ setGeneric("celdaUmap",

 setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

     function(sce,

         useAssay = "counts",

+        altExpName = "featureSubset",

         maxCells = NULL,

         minClusterSize = 100,

         modules = NULL,

@@ -92,8 +95,9 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

         ...) {

         if (is.null(seed)) {

-            res <- .celdaUmap(sce = sce,

+            sce <- .celdaUmap(sce = sce,

                 useAssay = useAssay,

+                altExpName = altExpName,

                 maxCells = maxCells,

                 minClusterSize = minClusterSize,

                 modules = modules,

@@ -110,8 +114,9 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

                 ...)

         } else {

             with_seed(seed,

-                res <- .celdaUmap(sce = sce,

+                sce <- .celdaUmap(sce = sce,

                     useAssay = useAssay,

+                    altExpName = altExpName,

                     maxCells = maxCells,

                     minClusterSize = minClusterSize,

                     modules = modules,

@@ -127,8 +132,6 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

                     cores = cores,

                     ...))

         }

-

-        SingleCellExperiment::reducedDim(sce, "celda_UMAP") <- res

         return(sce)

     })

@@ -151,9 +154,10 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

     ...) {

     celdaMod <- celdaModel(sce)

+    altExp <- SingleCellExperiment::altExp(sce, altExpName)

     if (celdaMod == "celda_C") {

-        res <- .celdaUmapC(sce = sce,

+        res <- .celdaUmapC(sce = altExp,

             useAssay = useAssay,

             maxCells = maxCells,

             minClusterSize = minClusterSize,

@@ -168,7 +172,7 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

             cores = cores,

             ...)

     } else if (celdaMod == "celda_CG") {

-        res <- .celdaUmapCG(sce = sce,

+        res <- .celdaUmapCG(sce = altExp,

             useAssay = useAssay,

             maxCells = maxCells,

             minClusterSize = minClusterSize,

@@ -183,7 +187,7 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

             cores = cores,

             ...)

     } else if (celdaMod == "celda_G") {

-        res <- .celdaUmapG(sce = sce,

+        res <- .celdaUmapG(sce = altExp,

             useAssay = useAssay,

             maxCells = maxCells,

             minClusterSize = minClusterSize,

@@ -198,10 +202,12 @@ setMethod("celdaUmap", signature(sce = "SingleCellExperiment"),

             cores = cores,

             ...)

     } else {

-        stop("S4Vectors::metadata(sce)$celda_parameters$model must be",

+        stop("S4Vectors::metadata(altExp(sce, altExpName))$",

+            "celda_parameters$model must be",

             " one of 'celda_C', 'celda_G', or 'celda_CG'")

     }

-    return(res)

+    SingleCellExperiment::reducedDim(sce, "celda_UMAP") <- res

+    return(sce)

 }

@@ -1,13 +1,20 @@

 #' @title Cell clustering with Celda

 #' @description Clusters the columns of a count matrix containing single-cell

-#'  data into K subpopulations.

+#'  data into K subpopulations. The

+#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in

+#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if

+#'  it exists. Otherwise, the \code{useAssay}

+#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if

+#'  \code{x} is a \linkS4class{SingleCellExperiment} object.

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

-#'  with the matrix located in the assay slot under \code{useAssay}.

+#'  with the matrix located in the assay slot under \code{useAssay} in

+#'  \code{altExp(x, altExpName)}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

-#'  slot to use if \code{x} is a

-#'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".

+#' @param useAssay A string specifying the name of the

+#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".

+#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#'  to use. Default "featureSubset".

 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell

 #'  (column) in the count matrix.

 #' @param K Integer. Number of cell populations.

@@ -79,6 +86,7 @@ setMethod("celda_C",

     signature(x = "SingleCellExperiment"),

     function(x,

         useAssay = "counts",

+        altExpName = "featureSubset",

         sampleLabel = NULL,

         K,

         alpha = 1,

@@ -97,12 +105,24 @@ setMethod("celda_C",

         verbose = TRUE) {

         xClass <- "SingleCellExperiment"

-        counts <- SummarizedExperiment::assay(x, i = useAssay)

-        sce <- .celdaCWithSeed(counts = counts,

+        if (!altExpName %in% SingleCellExperiment::altExpNames(x)) {

+            stop(altExpName, " not in 'altExpNames(x)'. Run ",

+                "selectFeatures(x) first!")

+        }

+

+        altExp <- SingleCellExperiment::altExp(x, altExpName)

+

+        if (!useAssay %in% SummarizedExperiment::assayNames(altExp)) {

+            stop(useAssay, " not in assayNames(altExp(x, altExpName))")

+        }

+

+        counts <- SummarizedExperiment::assay(altExp, i = useAssay)

+

+        altExp <- .celdaCWithSeed(counts = counts,

             xClass = xClass,

             useAssay = useAssay,

-            sce = x,

+            sce = altExp,

             sampleLabel = sampleLabel,

             K = K,

             alpha = alpha,

@@ -119,7 +139,8 @@ setMethod("celda_C",

             zInit = zInit,

             logfile = logfile,

             verbose = verbose)

-        return(sce)

+        SingleCellExperiment::altExp(x, altExpName) <- altExp

+        return(x)

     }

 )

@@ -129,6 +150,8 @@ setMethod("celda_C",

 setMethod("celda_C",

     signature(x = "matrix"),

     function(x,

+        useAssay = "counts",

+        altExpName = "featureSubset",

         sampleLabel = NULL,

         K,

         alpha = 1,

@@ -146,14 +169,16 @@ setMethod("celda_C",

         logfile = NULL,

         verbose = TRUE) {

+        ls <- list()

+        ls[[useAssay]] <- x