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fix doc warning file link in package does not exist and so has been treated as a topic

zhewa authored on 16/10/2020 21:36:32
Showing 70 changed files

... ...
@@ -1,6 +1,6 @@
1 1
 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.5.10
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+Version: 1.5.11
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")),
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@@ -8,10 +8,10 @@
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 #'  \item A \linkS4class{SingleCellExperiment} object returned by
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 #'  \link{celda_C}, or \link{celda_CG}, with the matrix
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 #'  located in the \code{useAssay} assay slot. The
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-#'  a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will
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+#'  a \link{altExp} slot with name \code{altExpName} will
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 #'  be used. Rows represent features and columns represent cells.
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 #'  \item Celda model object.}
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param value Character vector of cell cluster labels for replacements. Works
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 #'  only if \code{x} is a \linkS4class{SingleCellExperiment} object.
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@@ -85,7 +85,7 @@ setReplaceMethod("celdaClusters", signature(x = "SingleCellExperiment"),
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 #'  \link{celda_G}, or \link{celda_CG}, with the matrix
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 #'  located in the \code{useAssay} assay slot.
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 #'  Rows represent features and columns represent cells.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param value Character vector of feature module labels for replacements.
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 #'  Works only if \code{x} is a \linkS4class{SingleCellExperiment} object.
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@@ -141,7 +141,7 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"),
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 #'  located in the \code{useAssay} assay slot.
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 #'  Rows represent features and columns represent cells.
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 #'  \item A celda model object.}
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param value Character vector of sample labels for replacements. Works
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 #'  only is \code{x} is a \linkS4class{SingleCellExperiment} object.
... ...
@@ -263,7 +263,7 @@ setMethod("matrixNames",
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 #'  priors from the celdaList object when it was created.
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 #' @param x An object of class \linkS4class{SingleCellExperiment} or class
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 #'  \code{celdaList}.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return Data Frame. Contains details on the various K/L parameters, chain
... ...
@@ -310,7 +310,7 @@ setMethod("runParams",
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 #'  \link{celdaGridSearch} run.
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 #' @param x An object of class \linkS4class{SingleCellExperiment} or
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 #'  \code{celdaList}.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return List. Contains one celdaModel object for each of the parameters
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@@ -357,7 +357,7 @@ setMethod("resList",
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 #'  \link{celda_C}, \link{celda_G} or \link{celda_CG}.
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 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return Character. The celda model. Can be one of "celda_C", "celda_G", or
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@@ -12,8 +12,8 @@
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 #'  with the matrix located in the assay slot under \code{useAssay}.
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 #'  Rows represent features and columns represent cells.
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 #' @param useAssay A string specifying the name of the
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-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#'  \link{assay} slot to use. Default "counts".
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param model Celda model. Options available in \link{availableModels}.
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 #' @param paramsTest List. A list denoting the combinations of parameters to
... ...
@@ -45,7 +45,7 @@
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 #'  and main process. Default "Celda".
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 #' @return A \linkS4class{SingleCellExperiment} object. Function
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 #'  parameter settings and celda model results are stored in the
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-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot.
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+#'  \link{metadata} \code{"celda_grid_search"} slot.
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @seealso \link{celda_G} for feature clustering, \link{celda_C} for
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 #'  clustering of cells, and \link{celda_CG} for simultaneous clustering of
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@@ -440,7 +440,7 @@ setMethod("celdaGridSearch",
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 #'  \item celdaList object.}
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 #' @param params List. List of parameters used to subset the matching celda
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 #'  models in list \code{"celda_grid_search"} in \code{metadata(x)}.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return One of
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@@ -451,10 +451,10 @@ setMethod("celdaGridSearch",
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 #'  \code{"celda_grid_search"} slot in \code{metadata(x)} matches
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 #'  the given criteria, a new \linkS4class{SingleCellExperiment} object
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 #'  with the matching model stored in the
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-#'  \link[S4Vectors]{metadata}
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+#'  \link{metadata}
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 #'  \code{"celda_parameters"} slot will be returned. Otherwise, a new
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 #'  \linkS4class{SingleCellExperiment} object with the subset models stored
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-#'  in the \link[S4Vectors]{metadata}
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+#'  in the \link{metadata}
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 #'  \code{"celda_grid_search"} slot will be returned.
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 #'  \item A new \code{celdaList} object containing all models matching the
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 #'  provided criteria in \code{params}. If only one item in the
... ...
@@ -581,7 +581,7 @@ setMethod("subsetCeldaList",
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 #'  best model as a
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 #'  \code{celdaList} object or not. If \code{FALSE}, return the best model as a
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 #'  corresponding celda model object.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return One of
... ...
@@ -591,10 +591,10 @@ setMethod("subsetCeldaList",
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 #'  \code{metadata(x)}. If there is only one set of parameters,
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 #'  a new \linkS4class{SingleCellExperiment} object
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 #'  with the matching model stored in the
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-#'  \link[S4Vectors]{metadata}
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+#'  \link{metadata}
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 #'  \code{"celda_parameters"} slot will be returned. Otherwise, a new
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 #'  \linkS4class{SingleCellExperiment} object with the subset models stored
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-#'  in the \link[S4Vectors]{metadata}
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+#'  in the \link{metadata}
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 #'  \code{"celda_grid_search"} slot will be returned.
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 #'  \item A new \code{celdaList} object containing one model with the best
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 #'  log-likelihood for each set of parameters. If only one set of parameters
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@@ -4,9 +4,9 @@
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 #'  populations and samples).
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 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.
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-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
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+#' @param useAssay A string specifying which \link{assay}
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 #'  slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param level Character. One of "cellPopulation" or "Sample".
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 #'  "cellPopulation" will display the absolute probabilities and relative
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@@ -8,9 +8,9 @@
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 #'  transformed before applying UMAP.
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 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object
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 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.
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-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
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+#' @param useAssay A string specifying which \link{assay}
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 #'  slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param maxCells Integer. Maximum number of cells to plot. Cells will be
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 #'  randomly subsampled if \code{ncol(sce) > maxCells}. Larger numbers of cells
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@@ -62,7 +62,7 @@
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 #' @param ... Additional parameters to pass to \link[uwot]{umap}.
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 #' @return \code{sce} with UMAP coordinates
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 #'  (columns "celda_UMAP1" & "celda_UMAP2") added to
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-#'  \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}.
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+#'  \code{\link{reducedDim}(sce, "celda_UMAP")}.
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 #' @export
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 setGeneric("celdaUmap",
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     function(sce, ...) {
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@@ -1,10 +1,10 @@
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 #' @title Cell clustering with Celda
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 #' @description Clusters the columns of a count matrix containing single-cell
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 #'  data into K subpopulations. The
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-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in
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-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
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+#'  \code{useAssay} \link{assay} slot in
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+#'  \code{altExpName} \link{altExp} slot will be used if
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 #'  it exists. Otherwise, the \code{useAssay}
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-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
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+#'  \link{assay} slot in \code{x} will be used if
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 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.
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 #' @param x A numeric \link{matrix} of counts or a
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 #'  \linkS4class{SingleCellExperiment}
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@@ -12,8 +12,8 @@
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 #'  \code{altExp(x, altExpName)}.
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 #'  Rows represent features and columns represent cells.
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 #' @param useAssay A string specifying the name of the
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-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#'  \link{assay} slot to use. Default "counts".
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell
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 #'  (column) in the count matrix.
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@@ -59,10 +59,10 @@
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 #' @param verbose Logical. Whether to print log messages. Default TRUE.
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object. Function
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-#'  parameter settings are stored in the \link[S4Vectors]{metadata}
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+#'  parameter settings are stored in the \link{metadata}
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 #'  \code{"celda_parameters"} slot.
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 #'  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in
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-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell
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+#'  \link{colData} contain sample labels and celda cell
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 #'  population clusters.
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 #' @seealso \link{celda_G} for feature clustering and \link{celda_CG} for
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 #'  simultaneous clustering of features and cells. \link{celdaGridSearch} can
... ...
@@ -1,19 +1,19 @@
1 1
 #' @title Cell and feature clustering with Celda
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 #' @description Clusters the rows and columns of a count matrix containing
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 #'  single-cell data into L modules and K subpopulations, respectively. The
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-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in
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-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
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+#'  \code{useAssay} \link{assay} slot in
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+#'  \code{altExpName} \link{altExp} slot will be used if
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 #'  it exists. Otherwise, the \code{useAssay}
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-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
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+#'  \link{assay} slot in \code{x} will be used if
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 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.
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 #' @param x A numeric \link{matrix} of counts or a
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 #'  \linkS4class{SingleCellExperiment}
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-#'  with the matrix located in the \link[SummarizedExperiment]{assay}
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+#'  with the matrix located in the \link{assay}
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 #'  slot under \code{useAssay} in \code{altExp(x, altExpName)}.
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 #'  Rows represent features and columns represent cells.
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 #' @param useAssay A string specifying the name of the
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-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#'  \link{assay} slot to use. Default "counts".
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell
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 #'  (column) in the count matrix.
... ...
@@ -35,11 +35,12 @@
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 #'  likelihood to stop inference. Default 10.
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 #' @param maxIter Integer. Maximum number of iterations of Gibbs sampling to
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 #'  perform. Default 200.
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-#' @param splitOnIter Integer. On every `splitOnIter` iteration, a heuristic
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+#' @param splitOnIter Integer. On every \code{splitOnIter} iteration,
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+#'  a heuristic
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 #'  will be applied to determine if a cell population or feature module should
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 #'  be reassigned and another cell population or feature module should be split
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 #'  into two clusters. To disable splitting, set to -1. Default 10.
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-#' @param splitOnLast Integer. After `stopIter` iterations have been
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+#' @param splitOnLast Integer. After \code{stopIter} iterations have been
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 #'  performed without improvement, a heuristic will be applied to determine if
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 #'  a cell population or feature module should be reassigned and another cell
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 #'  population or feature module should be split into two clusters. If a split
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@@ -52,32 +53,32 @@
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 #'  With 'random', cells are randomly assigned to a populations. With 'split',
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 #'  cells will be split into sqrt(K) populations and then each popluation will
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 #'  be subsequently split into another sqrt(K) populations. With 'predefined',
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-#'  values in `zInit` will be used to initialize `z`. Default 'split'.
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+#'  values in \code{zInit} will be used to initialize \code{z}. Default 'split'.
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 #' @param yInitialize Chararacter. One of 'random', 'split', or 'predefined'.
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 #'  With 'random', features are randomly assigned to a modules. With 'split',
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 #'  features will be split into sqrt(L) modules and then each module will be
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 #'  subsequently split into another sqrt(L) modules. With 'predefined', values
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-#'  in `yInit` will be used to initialize `y`. Default 'split'.
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+#'  in \code{yInit} will be used to initialize \code{y}. Default 'split'.
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 #' @param zInit Integer vector. Sets initial starting values of z. If NULL,
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 #'  starting values for each cell will be randomly sampled from 1:K. 'zInit'
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-#'  can only be used when `initialize' = 'random'`. Default NULL.
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+#'  can only be used when \code{initialize = "random"}. Default NULL.
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 #' @param yInit Integer vector. Sets initial starting values of y. If NULL,
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 #'  starting values for each feature will be randomly sampled from 1:L.
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-#'  'yInit' can only be used when `initialize = 'random'`. Default NULL.
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-#' @param countChecksum Character. An MD5 checksum for the `counts` matrix.
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+#'  'yInit' can only be used when \code{initialize = "random"}. Default NULL.
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+#' @param countChecksum Character. An MD5 checksum for the counts matrix.
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 #'  Default NULL.
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 #' @param logfile Character. Messages will be redirected to a file named
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 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.
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 #' @param verbose Logical. Whether to print log messages. Default TRUE.
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return A \linkS4class{SingleCellExperiment} object. Function
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-#'  parameter settings are stored in \link[S4Vectors]{metadata}
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-#'  \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot.
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-#'  In \link[SingleCellExperiment]{altExp} slot,
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+#'  parameter settings are stored in \link{metadata}
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+#'  \code{"celda_parameters"} in \link{altExp} slot.
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+#'  In \link{altExp} slot,
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 #'  columns \code{celda_sample_label} and \code{celda_cell_cluster} in
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-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell
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+#'  \link{colData} contain sample labels and celda cell
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 #'  population clusters. Column \code{celda_feature_module} in
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-#'  \link[SummarizedExperiment]{rowData} contains feature modules.
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+#'  \link{rowData} contains feature modules.
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 #' @seealso \link{celda_G} for feature clustering and \link{celda_C} for
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 #'  clustering cells. \link{celdaGridSearch} can be used to run multiple
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 #'  values of K/L and multiple chains in parallel.
... ...
@@ -1,18 +1,18 @@
1 1
 #' @title Feature clustering with Celda
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 #' @description Clusters the rows of a count matrix containing single-cell data
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 #'  into L modules. The
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-#'  \code{useAssay} \link[SummarizedExperiment]{assay} slot in
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-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
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+#'  \code{useAssay} \link{assay} slot in
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+#'  \code{altExpName} \link{altExp} slot will be used if
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 #'  it exists. Otherwise, the \code{useAssay}
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-#'  \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
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+#'  \link{assay} slot in \code{x} will be used if
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 #'  \code{x} is a \linkS4class{SingleCellExperiment} object.
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 #' @param x A numeric \link{matrix} of counts or a
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 #'  \linkS4class{SingleCellExperiment}
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 #'  with the matrix located in the assay slot under \code{useAssay}.
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 #'  Rows represent features and columns represent cells.
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 #' @param useAssay A string specifying the name of the
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-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#'  \link{assay} slot to use. Default "counts".
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @param L Integer. Number of feature modules.
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 #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to
... ...
@@ -53,9 +53,9 @@
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 #' @param verbose Logical. Whether to print log messages. Default TRUE.
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 #' @param ... Ignored. Placeholder to prevent check warning.
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 #' @return A \linkS4class{SingleCellExperiment} object. Function
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-#'  parameter settings are stored in the \link[S4Vectors]{metadata}
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+#'  parameter settings are stored in the \link{metadata}
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 #'  \code{"celda_parameters"} slot. Column \code{celda_feature_module} in
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-#'  \link[SummarizedExperiment]{rowData} contains feature modules.
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+#'  \link{rowData} contains feature modules.
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 #' @seealso \link{celda_C} for cell clustering and \link{celda_CG} for
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 #'  simultaneous clustering of features and cells. \link{celdaGridSearch} can
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 #'  be used to run multiple values of L and multiple chains in parallel.
... ...
@@ -137,7 +137,7 @@ normalizeCounts <- function(counts,
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 #' @param sce \linkS4class{SingleCellExperiment} object returned from
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 #'  \link{celda_C} or \link{celda_CG}. Must contain column
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 #'  \code{celda_cell_cluster} in
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-#'  \code{\link[SummarizedExperiment]{colData}(altExp(sce, altExpName))}.
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+#'  \code{\link{colData}(altExp(sce, altExpName))}.
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 #' @param from Numeric vector. Unique values in the range of
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 #'  \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to
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 #'  the original cluster
... ...
@@ -145,7 +145,7 @@ normalizeCounts <- function(counts,
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 #' @param to Numeric vector. Unique values in the range of
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 #'  \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to
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 #'  the new cluster labels.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
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+#' @param altExpName The name for the \link{altExp} slot
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 #'  to use. Default "featureSubset".
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 #' @return \linkS4class{SingleCellExperiment} object with recoded cell
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 #'  cluster labels.
... ...
@@ -188,13 +188,13 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") {
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 #' @param sce \linkS4class{SingleCellExperiment} object returned from
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 #'  \link{celda_G} or \link{celda_CG}. Must contain column
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 #'  \code{celda_feature_module} in
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-#'  \code{\link[SummarizedExperiment]{rowData}(altExp(sce, altExpName))}.
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+#'  \code{\link{rowData}(altExp(sce, altExpName))}.
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 #' @param from Numeric vector. Unique values in the range of
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 #'  \code{seq(celdaModules(sce))} that correspond to the original module labels
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 #'  in \code{sce}.
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 #' @param to Numeric vector. Unique values in the range of
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 #'  \code{seq(celdaModules(sce))} that correspond to the new module labels.
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-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
197
+#' @param altExpName The name for the \link{altExp} slot
198 198
 #'  to use. Default "featureSubset".
199 199
 #' @return @return \linkS4class{SingleCellExperiment} object with recoded
200 200
 #'  feature module labels.
... ...
@@ -525,9 +525,9 @@ distinctColors <- function(n,
525 525
 #'  \link{celda_G}, or \link{celda_CG}, with the matrix
526 526
 #'  located in the \code{useAssay} assay slot.
527 527
 #'  Rows represent features and columns represent cells.
528
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
528
+#' @param useAssay A string specifying which \link{assay}
529 529
 #'  slot to use. Default "counts".
530
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
530
+#' @param altExpName The name for the \link{altExp} slot
531 531
 #'  to use. Default "featureSubset".
532 532
 #' @param outputFile File name for feature module table. If NULL, file will
533 533
 #'  not be created. Default NULL.
... ...
@@ -3,9 +3,9 @@
3 3
 #'  clustering results.
4 4
 #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object
5 5
 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.
6
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
6
+#' @param useAssay A string specifying which \link{assay}
7 7
 #'  slot to use. Default "counts".
8
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
8
+#' @param altExpName The name for the \link{altExp} slot
9 9
 #'  to use. Default "featureSubset".
10 10
 #' @param featureIx Integer vector. Select features for display in heatmap. If
11 11
 #'  NULL, no subsetting will be performed. Default NULL. \strong{Only used for
... ...
@@ -8,9 +8,9 @@
8 8
 #'  Module probabilities are square-root transformed before applying tSNE.
9 9
 #' @param sce A \linkS4class{SingleCellExperiment} object
10 10
 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.
11
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
11
+#' @param useAssay A string specifying which \link{assay}
12 12
 #'  slot to use. Default "counts".
13
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
13
+#' @param altExpName The name for the \link{altExp} slot
14 14
 #'  to use. Default "featureSubset".
15 15
 #' @param maxCells Integer. Maximum number of cells to plot. Cells will be
16 16
 #'  randomly subsampled if \code{ncol(counts) > maxCells}. Larger numbers of
... ...
@@ -48,7 +48,7 @@
48 48
 #' @param ... Ignored. Placeholder to prevent check warning.
49 49
 #' @return \code{sce} with t-SNE coordinates
50 50
 #'  (columns "celda_tSNE1" & "celda_tSNE2") added to
51
-#'  \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}.
51
+#'  \code{\link{reducedDim}(sce, "celda_tSNE")}.
52 52
 #' @export
53 53
 setGeneric("celdaTsne",
54 54
     function(sce, ...) {
... ...
@@ -11,17 +11,17 @@
11 11
 #'  \code{celdaModel}. Dimensions and MD5 checksum will be checked by
12 12
 #'  \link{compareCountMatrix}.
13 13
 #' @param useAssay A string specifying the name of the
14
-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
15
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
14
+#'  \link{assay} slot to use. Default "counts".
15
+#' @param altExpName The name for the \link{altExp} slot
16 16
 #'  to use. Default "featureSubset".
17 17
 #' @param ... Ignored. Placeholder to prevent check warning.
18 18
 #' @return A \linkS4class{SingleCellExperiment} object. Function
19
-#'  parameter settings are stored in the \link[S4Vectors]{metadata}
19
+#'  parameter settings are stored in the \link{metadata}
20 20
 #'  \code{"celda_parameters"} slot.
21 21
 #'  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in
22
-#'  \link[SummarizedExperiment]{colData} contain sample labels and celda cell
22
+#'  \link{colData} contain sample labels and celda cell
23 23
 #'  population clusters. Column \code{celda_feature_module} in
24
-#'  \link[SummarizedExperiment]{rowData} contain feature modules.
24
+#'  \link{rowData} contain feature modules.
25 25
 #' @export
26 26
 setGeneric("celdatosce", function(celdaModel, counts, ...) {
27 27
     standardGeneric("celdatosce")})
... ...
@@ -8,9 +8,9 @@
8 8
 #'  \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix
9 9
 #'  located in the \code{useAssay} assay slot.
10 10
 #'  Rows represent features and columns represent cells.
11
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
11
+#' @param useAssay A string specifying which \link{assay}
12 12
 #'  slot to use. Default "counts".
13
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
13
+#' @param altExpName The name for the \link{altExp} slot
14 14
 #'  to use. Default "featureSubset".
15 15
 #' @param log Logical. If \code{FALSE}, then the normalized conditional
16 16
 #'  probabilities will be returned. If \code{TRUE}, then the unnormalized log
... ...
@@ -7,10 +7,10 @@
7 7
 #'  Rows represent features and columns represent cells. Must contain cluster
8 8
 #'  labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a
9 9
 #'  \linkS4class{SingleCellExperiment} object.
10
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
10
+#' @param useAssay A string specifying which \link{assay}
11 11
 #'  slot to use if \code{x} is a
12 12
 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".
13
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
13
+#' @param altExpName The name for the \link{altExp} slot
14 14
 #'  to use. Default "featureSubset".
15 15
 #' @param celdaMod Celda object of class `celda_C` or `celda_CG`.
16 16
 #' @param c1 Integer vector. Cell populations to include in group 1 for the
... ...
@@ -11,10 +11,10 @@
11 11
 #'  \item Integer counts matrix. Rows represent features and columns represent
12 12
 #'  cells. This matrix should be the same as the one used to generate
13 13
 #'  \code{celdaMod}.}
14
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
14
+#' @param useAssay A string specifying which \link{assay}
15 15
 #'  slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.
16 16
 #'  Default "counts".
17
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
17
+#' @param altExpName The name for the \link{altExp} slot
18 18
 #'  to use. Default "featureSubset".
19 19
 #' @param celdaMod Celda model object. Only works if \code{x} is an integer
20 20
 #'  counts matrix.
... ...
@@ -8,7 +8,7 @@
8 8
 #'  Rows represent features and columns represent cells.
9 9
 #' @param feature Character vector. Identify feature modules for the specified
10 10
 #'  feature names. \code{feature} must match the rownames of \code{sce}.
11
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
11
+#' @param altExpName The name for the \link{altExp} slot
12 12
 #'  to use. Default "featureSubset".
13 13
 #' @param exactMatch Logical. Whether to look for exactMatch of the gene name
14 14
 #'  within counts matrix. Default \code{TRUE}.
... ...
@@ -9,10 +9,10 @@
9 9
 #'  \linkS4class{SingleCellExperiment}
10 10
 #'  with the matrix located in the assay slot under \code{useAssay}.
11 11
 #'  Rows represent features and columns represent cells.
12
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
12
+#' @param useAssay A string specifying which \link{assay}
13 13
 #'  slot to use if \code{x} is a
14 14
 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".
15
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
15
+#' @param altExpName The name for the \link{altExp} slot
16 16
 #'  to use. Default "featureSubset".
17 17
 #' @param class Vector of cell cluster labels.
18 18
 #' @param oneoffMetric A character string. What one-off metric to run, either
... ...
@@ -9,10 +9,10 @@
9 9
 #'  with the matrix located in the assay slot under \code{useAssay}.
10 10
 #'  Rows represent features and columns represent cells. Rownames of the
11 11
 #'  matrix or \linkS4class{SingleCellExperiment} object should be gene names.
12
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
12
+#' @param useAssay A string specifying which \link{assay}
13 13
 #'  slot to use if \code{x} is a
14 14
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
15
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
15
+#' @param altExpName The name for the \link{altExp} slot
16 16
 #'  to use. Default "featureSubset".
17 17
 #' @param celdaModel Celda object of class \code{celda_G} or \code{celda_CG}.
18 18
 #' @param databases Character vector. Name of reference database. Available
... ...
@@ -5,9 +5,9 @@
5 5
 #'  \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix
6 6
 #'  located in the \code{useAssay} assay slot.
7 7
 #'  Rows represent features and columns represent cells.
8
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
8
+#' @param useAssay A string specifying which \link{assay}
9 9
 #'  slot to use. Default "counts".
10
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
10
+#' @param altExpName The name for the \link{altExp} slot
11 11
 #'  to use. Default "featureSubset".
12 12
 #' @param celdaMod celda model object. Ignored if \code{x} is a
13 13
 #'  \linkS4class{SingleCellExperiment} object.
... ...
@@ -154,7 +154,7 @@ setMethod("logLikelihood", signature(x = "matrix", celdaMod = "celda_CG"),
154 154
 #' @param x A \linkS4class{SingleCellExperiment} object
155 155
 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda
156 156
 #'  model object.
157
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
157
+#' @param altExpName The name for the \link{altExp} slot
158 158
 #'  to use. Default "featureSubset".
159 159
 #' @param ... Ignored. Placeholder to prevent check warning.
160 160
 #' @return Numeric. The log-likelihood at each step of Gibbs sampling used to
... ...
@@ -205,7 +205,7 @@ setMethod("logLikelihoodHistory",
205 205
 #' @param x A \linkS4class{SingleCellExperiment} object
206 206
 #'  returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda
207 207
 #'  model object.
208
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
208
+#' @param altExpName The name for the \link{altExp} slot
209 209
 #'  to use. Default "featureSubset".
210 210
 #' @param ... Ignored. Placeholder to prevent check warning.
211 211
 #' @export
... ...
@@ -10,10 +10,10 @@
10 10
 #'  \linkS4class{SingleCellExperiment}
11 11
 #'  with the matrix located in the assay slot under \code{useAssay}.
12 12
 #'  Rows represent features and columns represent cells.
13
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
13
+#' @param useAssay A string specifying which \link{assay}
14 14
 #'  slot to use if \code{x} is a
15 15
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
16
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
16
+#' @param altExpName The name for the \link{altExp} slot
17 17
 #'  to use. Default "featureSubset".
18 18
 #' @param featureModule Integer Vector. The featureModule(s) to display.
19 19
 #'  Multiple modules can be included in a vector. Default \code{NULL} which
... ...
@@ -10,10 +10,10 @@
10 10
 #'  \item Integer counts matrix. Rows represent features and columns represent
11 11
 #'  cells. This matrix should be the same as the one used to generate
12 12
 #'  \code{celdaMod}.}
13
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
13
+#' @param useAssay A string specifying which \link{assay}
14 14
 #'  slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.
15 15
 #'  Default "counts".
16
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
16
+#' @param altExpName The name for the \link{altExp} slot
17 17
 #'  to use. Default "featureSubset".
18 18
 #' @param celdaMod Celda model object. Only works if \code{x} is an integer
19 19
 #'  counts matrix.
... ...
@@ -347,10 +347,10 @@ setMethod(
347 347
 #'  Rows represent features and columns represent cells. Must contain
348 348
 #'  "celda_grid_search" slot in \code{metadata(x)} if \code{x} is a
349 349
 #'  \linkS4class{SingleCellExperiment} object.
350
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
350
+#' @param useAssay A string specifying which \link{assay}
351 351
 #'  slot to use if \code{x} is a
352 352
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
353
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
353
+#' @param altExpName The name for the \link{altExp} slot
354 354
 #'  to use. Default "featureSubset".
355 355
 #' @param celdaList Object of class 'celdaList'. Used only if \code{x} is a
356 356
 #'  matrix object.
... ...
@@ -483,7 +483,7 @@ setMethod("resamplePerplexity",
483 483
 #'  or \code{recursiveSplitCell}. Must contain a list named
484 484
 #'  \code{"celda_grid_search"} in \code{metadata(x)}.
485 485
 #'  \item celdaList object.}
486
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
486
+#' @param altExpName The name for the \link{altExp} slot
487 487
 #'  to use. Default "featureSubset".
488 488
 #' @param sep Numeric. Breaks in the x axis of the resulting plot.
489 489
 #' @param ... Ignored. Placeholder to prevent check warning.
... ...
@@ -743,7 +743,7 @@ setMethod("plotGridSearchPerplexity",
743 743
 #'  or \code{recursiveSplitCell}. Must contain a list named
744 744
 #'  \code{"celda_grid_search"} in \code{metadata(x)}.
745 745
 #'  \item celdaList object.}
746
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
746
+#' @param altExpName The name for the \link{altExp} slot
747 747
 #'  to use. Default "featureSubset".
748 748
 #' @param sep Numeric. Breaks in the x axis of the resulting plot.
749 749
 #' @param n Integer. Width of the rolling window. Default 10.
... ...
@@ -12,15 +12,15 @@
12 12
 #'  reduction output.
13 13
 #' @param dim2 Numeric vector. Second dimension from data dimension
14 14
 #'  reduction output.
15
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
15
+#' @param useAssay A string specifying which \link{assay}
16 16
 #'  slot to use if \code{x} is a
17 17
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
18
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
18
+#' @param altExpName The name for the \link{altExp} slot
19 19
 #'  to use. Default "featureSubset".
20 20
 #' @param size Numeric. Sets size of point on plot. Default 1.
21 21
 #' @param xlab Character vector. Label for the x-axis. Default 'Dimension_1'.
22 22
 #' @param ylab Character vector. Label for the y-axis. Default 'Dimension_2'.
23
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range
23
+#' @param limits Passed to \link{scale_colour_gradient2}. The range
24 24
 #'  of color scale.
25 25
 #' @param colorLow Character. A color available from `colors()`.
26 26
 #'  The color will be used to signify the lowest values on the scale.
... ...
@@ -291,10 +291,10 @@ setMethod("plotDimReduceGrid",
291 291
 #'  dimension reduction output.
292 292
 #' @param dim2 Numeric vector. Second dimension from data dimension
293 293
 #'  reduction output.
294
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
294
+#' @param useAssay A string specifying which \link{assay}
295 295
 #'  slot to use if \code{x} is a
296 296
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
297
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
297
+#' @param altExpName The name for the \link{altExp} slot
298 298
 #'  to use. Default "featureSubset".
299 299
 #' @param features Character vector. Features in the rownames of counts to plot.
300 300
 #' @param headers Character vector. If `NULL`, the corresponding rownames are
... ...
@@ -309,7 +309,7 @@ setMethod("plotDimReduceGrid",
309 309
 #' @param trim Numeric vector. Vector of length two that specifies the lower
310 310
 #'  and upper bounds for the data. This threshold is applied after row scaling.
311 311
 #'  Set to NULL to disable. Default \code{c(-1,1)}.
312
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range
312
+#' @param limits Passed to \link{scale_colour_gradient2}. The range
313 313
 #'  of color scale.
314 314
 #' @param size Numeric. Sets size of point on plot. Default 1.
315 315
 #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".
... ...
@@ -576,10 +576,10 @@ setMethod("plotDimReduceFeature",
576 576
 #'  First dimension from data dimension reduction output.
577 577
 #' @param dim2 Numeric vector.
578 578
 #'  Second dimension from data dimension reduction output.
579
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
579
+#' @param useAssay A string specifying which \link{assay}
580 580
 #'  slot to use if \code{x} is a
581 581
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
582
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
582
+#' @param altExpName The name for the \link{altExp} slot
583 583
 #'  to use. Default "featureSubset".
584 584
 #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if
585 585
 #'  \code{x} is a matrix object.
... ...
@@ -587,7 +587,7 @@ setMethod("plotDimReduceFeature",
587 587
 #'  e.g. c("1", "2").
588 588
 #' @param rescale Logical.
589 589
 #'  Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.
590
-#' @param limits Passed to \link[ggplot2]{scale_colour_gradient}. The range
590
+#' @param limits Passed to \link{scale_colour_gradient}. The range
591 591
 #'  of color scale.
592 592
 #' @param size Numeric. Sets size of point on plot. Default 1.
593 593
 #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".
... ...
@@ -814,7 +814,7 @@ setMethod("plotDimReduceModule",
814 814
 #'  \code{reducedDimNames(x)} if \code{x} is a
815 815
 #'  \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and
816 816
 #'  \code{dim2} are set.
817
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
817
+#' @param altExpName The name for the \link{altExp} slot
818 818
 #'  to use. Default "featureSubset".
819 819
 #' @param dim1 Numeric vector. First dimension from data
820 820
 #'  dimension reduction output.
... ...
@@ -1027,10 +1027,10 @@ setMethod("plotDimReduceCluster",
1027 1027
 #'  with the matrix located in the assay slot under \code{useAssay}. Rows
1028 1028
 #'  represent features and columns represent cells.
1029 1029
 #' @param features Character vector. Uses these genes for plotting.
1030
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
1030
+#' @param useAssay A string specifying which \link{assay}
1031 1031
 #'  slot to use if \code{x} is a
1032 1032
 #'  \linkS4class{SingleCellExperiment} object. Default "counts".
1033
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
1033
+#' @param altExpName The name for the \link{altExp} slot
1034 1034
 #'  to use. Default "featureSubset".
1035 1035
 #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if
1036 1036
 #'  \code{x} is a matrix object.
... ...
@@ -90,9 +90,9 @@
90 90
 #'  with the matrix located in the assay slot under \code{useAssay}.
91 91
 #'  Rows represent features and columns represent cells.
92 92
 #' @param useAssay A string specifying the name of the
93
-#'  \link[SummarizedExperiment]{assay}
93
+#'  \link{assay}
94 94
 #'  slot to use. Default "counts".
95
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
95
+#' @param altExpName The name for the \link{altExp} slot
96 96
 #'  to use. Default "featureSubset".
97 97
 #' @param sampleLabel Vector or factor. Denotes the sample label for each cell
98 98
 #'  (column) in the count matrix.
... ...
@@ -137,7 +137,7 @@
137 137
 #' @param ... Ignored. Placeholder to prevent check warning.
138 138
 #' @return A \linkS4class{SingleCellExperiment} object. Function
139 139
 #'  parameter settings and celda model results are stored in the
140
-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in
140
+#'  \link{metadata} \code{"celda_grid_search"} slot. The models in
141 141
 #'  the list will be of class \code{celda_C} if \code{yInit = NULL} or
142 142
 #'  \code{celda_CG} if \code{zInit} is set.
143 143
 #' @seealso \link{recursiveSplitModule} for recursive splitting of feature
... ...
@@ -859,10 +859,10 @@ setMethod("recursiveSplitCell",
859 859
 #'  \linkS4class{SingleCellExperiment}
860 860
 #'  with the matrix located in the assay slot under \code{useAssay}.
861 861
 #'  Rows represent features and columns represent cells.
862
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
862
+#' @param useAssay A string specifying which \link{assay}
863 863
 #'  slot to use if \code{x} is a
864 864
 #'  \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".
865
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
865
+#' @param altExpName The name for the \link{altExp} slot
866 866
 #'  to use. Default "featureSubset".
867 867
 #' @param initialL Integer. Minimum number of modules to try.
868 868
 #' @param maxL Integer. Maximum number of modules to try.
... ...
@@ -905,7 +905,7 @@ setMethod("recursiveSplitCell",
905 905
 #' @param ... Ignored. Placeholder to prevent check warning.
906 906
 #' @return A \linkS4class{SingleCellExperiment} object. Function
907 907
 #'  parameter settings and celda model results are stored in the
908
-#'  \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in
908
+#'  \link{metadata} \code{"celda_grid_search"} slot. The models in
909 909
 #'  the list will be of class \link{celda_G} if \code{zInit = NULL} or
910 910
 #'  \link{celda_CG} if \code{zInit} is set.
911 911
 #' @seealso \code{recursiveSplitCell} for recursive splitting of cell
... ...
@@ -3,8 +3,8 @@
3 3
 #'  Select features with at least \code{minCount} counts
4 4
 #'  in at least \code{minCell} cells. A \linkS4class{SingleCellExperiment}
5 5
 #'  object with subset features will be stored in the
6
-#'  \link[SingleCellExperiment]{altExp} slot with name \code{altExpName}.
7
-#'  The name of the \code{assay} slot in \link[SingleCellExperiment]{altExp}
6
+#'  \link{altExp} slot with name \code{altExpName}.
7
+#'  The name of the \code{assay} slot in \link{altExp}
8 8
 #'  will be the same as \code{useAssay}.
9 9
 #' @param x A numeric \link{matrix} of counts or a
10 10
 #'  \linkS4class{SingleCellExperiment}
... ...
@@ -13,13 +13,13 @@
13 13
 #' @param minCount Minimum number of counts required for feature selection.
14 14
 #' @param minCell Minimum number of cells required for feature selection.
15 15
 #' @param useAssay A string specifying the name of the
16
-#'  \link[SummarizedExperiment]{assay} slot to use. Default "counts".
17
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
16
+#'  \link{assay} slot to use. Default "counts".
17
+#' @param altExpName The name for the \link{altExp} slot
18 18
 #'  to use. Default "featureSubset".
19 19
 #' @param ... Ignored. Placeholder to prevent check warning.
20 20
 #' @return A \linkS4class{SingleCellExperiment} object with a
21
-#'  \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function
22
-#'  parameter settings are stored in the \link[S4Vectors]{metadata}
21
+#'  \code{altExpName} \link{altExp} slot. Function
22
+#'  parameter settings are stored in the \link{metadata}
23 23
 #'  \code{"select_features"} slot.
24 24
 #' @export
25 25
 setGeneric("selectFeatures", function(x, ...) {
... ...
@@ -41,13 +41,13 @@
41 41
 #'  \link[withr]{with_seed} are made.
42 42
 #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with
43 43
 #'  simulated count matrix stored in the "counts" assay slot. Function
44
-#'  parameter settings are stored in the \link[S4Vectors]{metadata} slot. For
44
+#'  parameter settings are stored in the \link{metadata} slot. For
45 45
 #'  \code{"celda_CG"} and \code{"celda_C"} models,
46 46
 #'  columns \code{celda_sample_label} and \code{celda_cell_cluster} in
47
-#'  \link[SummarizedExperiment]{colData} contain simulated sample labels and
47
+#'  \link{colData} contain simulated sample labels and
48 48
 #'  cell population clusters. For \code{"celda_CG"} and \code{"celda_G"}
49 49
 #'  models, column \code{celda_feature_module} in
50
-#'  \link[SummarizedExperiment]{rowData} contains simulated gene modules.
50
+#'  \link{rowData} contains simulated gene modules.
51 51
 #' @examples
52 52
 #' sce <- simulateCells()
53 53
 #' @export
... ...
@@ -5,9 +5,9 @@
5 5
 #' @param x A \linkS4class{SingleCellExperiment} object
6 6
 #'  with the matrix located in the assay slot under \code{useAssay}.
7 7
 #'  Rows represent features and columns represent cells.
8
-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}
8
+#' @param useAssay A string specifying which \link{assay}
9 9
 #'  slot to use for \code{x}. Default "counts".
10
-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot
10
+#' @param altExpName The name for the \link{altExp} slot
11 11
 #'  to use. Default "featureSubset".
12 12
 #' @param module Integer. The module to be split.
13 13
 #' @param n Integer. How many modules should \code{module} be split into.
... ...
@@ -18,7 +18,7 @@
18 18
 #' @param ... Ignored. Placeholder to prevent check warning.
19 19
 #' @return A updated \linkS4class{SingleCellExperiment} object with new
20 20
 #'  feature modules stored in column \code{celda_feature_module} in
21
-#'  \code{\link[SummarizedExperiment]{rowData}(x)}.
21
+#'  \code{\link{rowData}(x)}.
22 22
 #' @export
23 23
 setGeneric("splitModule",
24 24
     function(x, ...) {
... ...
@@ -19,7 +19,7 @@ model object.}
19 19
 
20 20
 \item{...}{Ignored. Placeholder to prevent check warning.}
21 21
 
22
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
22
+\item{altExpName}{The name for the \link{altExp} slot
23 23
 to use. Default "featureSubset".}
24 24
 }
25 25
 \value{
... ...
@@ -26,13 +26,13 @@ celdaClusters(x, altExpName = "featureSubset") <- value
26 26
 \item A \linkS4class{SingleCellExperiment} object returned by
27 27
 \link{celda_C}, or \link{celda_CG}, with the matrix
28 28
 located in the \code{useAssay} assay slot. The
29
-a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will
29
+a \link{altExp} slot with name \code{altExpName} will
30 30
 be used. Rows represent features and columns represent cells.
31 31
 \item Celda model object.}}
32 32
 
33 33
 \item{...}{Ignored. Placeholder to prevent check warning.}
34 34
 
35
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
35
+\item{altExpName}{The name for the \link{altExp} slot
36 36
 to use. Default "featureSubset".}
37 37
 
38 38
 \item{value}{Character vector of cell cluster labels for replacements. Works
... ...
@@ -51,9 +51,9 @@ Rows represent features and columns represent cells.}
51 51
 \item{...}{Ignored. Placeholder to prevent check warning.}
52 52
 
53 53
 \item{useAssay}{A string specifying the name of the
54
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}
54
+\link{assay} slot to use. Default "counts".}
55 55
 
56
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
56
+\item{altExpName}{The name for the \link{altExp} slot
57 57
 to use. Default "featureSubset".}
58 58
 
59 59
 \item{model}{Celda model. Options available in \link{availableModels}.}
... ...
@@ -98,7 +98,7 @@ and main process. Default "Celda".}
98 98
 \value{
99 99
 A \linkS4class{SingleCellExperiment} object. Function
100 100
  parameter settings and celda model results are stored in the
101
- \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot.
101
+ \link{metadata} \code{"celda_grid_search"} slot.
102 102
 }
103 103
 \description{
104 104
 Run Celda with different combinations of parameters and
... ...
@@ -22,10 +22,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}
22 22
 
23 23
 \item{...}{Additional parameters passed to \link{plotHeatmap}.}
24 24
 
25
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
25
+\item{useAssay}{A string specifying which \link{assay}
26 26
 slot to use. Default "counts".}
27 27
 
28
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
28
+\item{altExpName}{The name for the \link{altExp} slot
29 29
 to use. Default "featureSubset".}
30 30
 
31 31
 \item{featureIx}{Integer vector. Select features for display in heatmap. If
... ...
@@ -16,7 +16,7 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}
16 16
 
17 17
 \item{...}{Ignored. Placeholder to prevent check warning.}
18 18
 
19
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
19
+\item{altExpName}{The name for the \link{altExp} slot
20 20
 to use. Default "featureSubset".}
21 21
 }
22 22
 \value{
... ...
@@ -22,7 +22,7 @@ celdaModules(sce, altExpName = "featureSubset") <- value
22 22
 located in the \code{useAssay} assay slot.
23 23
 Rows represent features and columns represent cells.}
24 24
 
25
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
25
+\item{altExpName}{The name for the \link{altExp} slot
26 26
 to use. Default "featureSubset".}
27 27
 
28 28
 \item{value}{Character vector of feature module labels for replacements.
... ...
@@ -32,10 +32,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}
32 32
 
33 33
 \item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.}
34 34
 
35
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
35
+\item{useAssay}{A string specifying which \link{assay}
36 36
 slot to use. Default "counts".}
37 37
 
38
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
38
+\item{altExpName}{The name for the \link{altExp} slot
39 39
 to use. Default "featureSubset".}
40 40
 
41 41
 \item{level}{Character. One of "cellPopulation" or "Sample".
... ...
@@ -30,10 +30,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}
30 30
 
31 31
 \item{...}{Ignored. Placeholder to prevent check warning.}
32 32
 
33
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
33
+\item{useAssay}{A string specifying which \link{assay}
34 34
 slot to use. Default "counts".}
35 35
 
36
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
36
+\item{altExpName}{The name for the \link{altExp} slot
37 37
 to use. Default "featureSubset".}
38 38
 
39 39
 \item{maxCells}{Integer. Maximum number of cells to plot. Cells will be
... ...
@@ -82,7 +82,7 @@ a default value of 12345 is used. If NULL, no calls to
82 82
 \value{
83 83
 \code{sce} with t-SNE coordinates
84 84
  (columns "celda_tSNE1" & "celda_tSNE2") added to
85
- \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}.
85
+ \code{\link{reducedDim}(sce, "celda_tSNE")}.
86 86
 }
87 87
 \description{
88 88
 Embeds cells in two dimensions using \link[Rtsne]{Rtsne} based
... ...
@@ -34,10 +34,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.}
34 34
 
35 35
 \item{...}{Additional parameters to pass to \link[uwot]{umap}.}
36 36
 
37
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
37
+\item{useAssay}{A string specifying which \link{assay}
38 38
 slot to use. Default "counts".}
39 39
 
40
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
40
+\item{altExpName}{The name for the \link{altExp} slot
41 41
 to use. Default "featureSubset".}
42 42
 
43 43
 \item{maxCells}{Integer. Maximum number of cells to plot. Cells will be
... ...
@@ -103,7 +103,7 @@ be applied. Occurs after applying normalization and scale factor. Default
103 103
 \value{
104 104
 \code{sce} with UMAP coordinates
105 105
  (columns "celda_UMAP1" & "celda_UMAP2") added to
106
- \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}.
106
+ \code{\link{reducedDim}(sce, "celda_UMAP")}.
107 107
 }
108 108
 \description{
109 109
 Embeds cells in two dimensions using \link[uwot]{umap} based on
... ...
@@ -62,9 +62,9 @@ Rows represent features and columns represent cells.}
62 62
 \item{...}{Ignored. Placeholder to prevent check warning.}
63 63
 
64 64
 \item{useAssay}{A string specifying the name of the
65
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}
65
+\link{assay} slot to use. Default "counts".}
66 66
 
67
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
67
+\item{altExpName}{The name for the \link{altExp} slot
68 68
 to use. Default "featureSubset".}
69 69
 
70 70
 \item{sampleLabel}{Vector or factor. Denotes the sample label for each cell
... ...
@@ -127,19 +127,19 @@ can only be used when `initialize = 'random'`. Default NULL.}
127 127
 }
128 128
 \value{
129 129
 A \link[SingleCellExperiment]{SingleCellExperiment} object. Function
130
- parameter settings are stored in the \link[S4Vectors]{metadata}
130
+ parameter settings are stored in the \link{metadata}
131 131
  \code{"celda_parameters"} slot.
132 132
  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in
133
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell
133
+ \link{colData} contain sample labels and celda cell
134 134
  population clusters.
135 135
 }
136 136
 \description{
137 137
 Clusters the columns of a count matrix containing single-cell
138 138
  data into K subpopulations. The
139
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in
140
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
139
+ \code{useAssay} \link{assay} slot in
140
+ \code{altExpName} \link{altExp} slot will be used if
141 141
  it exists. Otherwise, the \code{useAssay}
142
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
142
+ \link{assay} slot in \code{x} will be used if
143 143
  \code{x} is a \linkS4class{SingleCellExperiment} object.
144 144
 }
145 145
 \examples{
... ...
@@ -65,16 +65,16 @@ celda_CG(x, ...)
65 65
 \arguments{
66 66
 \item{x}{A numeric \link{matrix} of counts or a
67 67
 \linkS4class{SingleCellExperiment}
68
-with the matrix located in the \link[SummarizedExperiment]{assay}
68
+with the matrix located in the \link{assay}
69 69
 slot under \code{useAssay} in \code{altExp(x, altExpName)}.
70 70
 Rows represent features and columns represent cells.}
71 71
 
72 72
 \item{...}{Ignored. Placeholder to prevent check warning.}
73 73
 
74 74
 \item{useAssay}{A string specifying the name of the
75
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}
75
+\link{assay} slot to use. Default "counts".}
76 76
 
77
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
77
+\item{altExpName}{The name for the \link{altExp} slot
78 78
 to use. Default "featureSubset".}
79 79
 
80 80
 \item{sampleLabel}{Vector or factor. Denotes the sample label for each cell
... ...
@@ -107,12 +107,13 @@ likelihood to stop inference. Default 10.}
107 107
 \item{maxIter}{Integer. Maximum number of iterations of Gibbs sampling to
108 108
 perform. Default 200.}
109 109
 
110
-\item{splitOnIter}{Integer. On every `splitOnIter` iteration, a heuristic
110
+\item{splitOnIter}{Integer. On every \code{splitOnIter} iteration,
111
+a heuristic
111 112
 will be applied to determine if a cell population or feature module should
112 113
 be reassigned and another cell population or feature module should be split
113 114
 into two clusters. To disable splitting, set to -1. Default 10.}
114 115
 
115
-\item{splitOnLast}{Integer. After `stopIter` iterations have been
116
+\item{splitOnLast}{Integer. After \code{stopIter} iterations have been
116 117
 performed without improvement, a heuristic will be applied to determine if
117 118
 a cell population or feature module should be reassigned and another cell
118 119
 population or feature module should be split into two clusters. If a split
... ...
@@ -128,24 +129,24 @@ a default value of 12345 is used. If NULL, no calls to
128 129
 With 'random', cells are randomly assigned to a populations. With 'split',
129 130
 cells will be split into sqrt(K) populations and then each popluation will
130 131
 be subsequently split into another sqrt(K) populations. With 'predefined',
131
-values in `zInit` will be used to initialize `z`. Default 'split'.}
132
+values in \code{zInit} will be used to initialize \code{z}. Default 'split'.}
132 133
 
133 134
 \item{yInitialize}{Chararacter. One of 'random', 'split', or 'predefined'.
134 135
 With 'random', features are randomly assigned to a modules. With 'split',
135 136
 features will be split into sqrt(L) modules and then each module will be
136 137
 subsequently split into another sqrt(L) modules. With 'predefined', values
137
-in `yInit` will be used to initialize `y`. Default 'split'.}
138
+in \code{yInit} will be used to initialize \code{y}. Default 'split'.}
138 139
 
139
-\item{countChecksum}{Character. An MD5 checksum for the `counts` matrix.
140
+\item{countChecksum}{Character. An MD5 checksum for the counts matrix.
140 141
 Default NULL.}
141 142
 
142 143
 \item{zInit}{Integer vector. Sets initial starting values of z. If NULL,
143 144
 starting values for each cell will be randomly sampled from 1:K. 'zInit'
144
-can only be used when `initialize' = 'random'`. Default NULL.}
145
+can only be used when \code{initialize = "random"}. Default NULL.}
145 146
 
146 147
 \item{yInit}{Integer vector. Sets initial starting values of y. If NULL,
147 148
 starting values for each feature will be randomly sampled from 1:L.
148
-'yInit' can only be used when `initialize = 'random'`. Default NULL.}
149
+'yInit' can only be used when \code{initialize = "random"}. Default NULL.}
149 150
 
150 151
 \item{logfile}{Character. Messages will be redirected to a file named
151 152
 `logfile`. If NULL, messages will be printed to stdout.  Default NULL.}
... ...
@@ -154,21 +155,21 @@ starting values for each feature will be randomly sampled from 1:L.
154 155
 }
155 156
 \value{
156 157
 A \linkS4class{SingleCellExperiment} object. Function
157
- parameter settings are stored in \link[S4Vectors]{metadata}
158
- \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot.
159
- In \link[SingleCellExperiment]{altExp} slot,
158
+ parameter settings are stored in \link{metadata}
159
+ \code{"celda_parameters"} in \link{altExp} slot.
160
+ In \link{altExp} slot,
160 161
  columns \code{celda_sample_label} and \code{celda_cell_cluster} in
161
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell
162
+ \link{colData} contain sample labels and celda cell
162 163
  population clusters. Column \code{celda_feature_module} in
163
- \link[SummarizedExperiment]{rowData} contains feature modules.
164
+ \link{rowData} contains feature modules.
164 165
 }
165 166
 \description{
166 167
 Clusters the rows and columns of a count matrix containing
167 168
  single-cell data into L modules and K subpopulations, respectively. The
168
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in
169
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
169
+ \code{useAssay} \link{assay} slot in
170
+ \code{altExpName} \link{altExp} slot will be used if
170 171
  it exists. Otherwise, the \code{useAssay}
171
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
172
+ \link{assay} slot in \code{x} will be used if
172 173
  \code{x} is a \linkS4class{SingleCellExperiment} object.
173 174
 }
174 175
 \examples{
... ...
@@ -59,9 +59,9 @@ Rows represent features and columns represent cells.}
59 59
 \item{...}{Ignored. Placeholder to prevent check warning.}
60 60
 
61 61
 \item{useAssay}{A string specifying the name of the
62
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}
62
+\link{assay} slot to use. Default "counts".}
63 63
 
64
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
64
+\item{altExpName}{The name for the \link{altExp} slot
65 65
 to use. Default "featureSubset".}
66 66
 
67 67
 \item{L}{Integer. Number of feature modules.}
... ...
@@ -118,17 +118,17 @@ starting values for each feature will be randomly sampled from `1:L`.
118 118
 }
119 119
 \value{
120 120
 A \linkS4class{SingleCellExperiment} object. Function
121
- parameter settings are stored in the \link[S4Vectors]{metadata}
121
+ parameter settings are stored in the \link{metadata}
122 122
  \code{"celda_parameters"} slot. Column \code{celda_feature_module} in
123
- \link[SummarizedExperiment]{rowData} contains feature modules.
123
+ \link{rowData} contains feature modules.
124 124
 }
125 125
 \description{
126 126
 Clusters the rows of a count matrix containing single-cell data
127 127
  into L modules. The
128
- \code{useAssay} \link[SummarizedExperiment]{assay} slot in
129
- \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if
128
+ \code{useAssay} \link{assay} slot in
129
+ \code{altExpName} \link{altExp} slot will be used if
130 130
  it exists. Otherwise, the \code{useAssay}
131
- \link[SummarizedExperiment]{assay} slot in \code{x} will be used if
131
+ \link{assay} slot in \code{x} will be used if
132 132
  \code{x} is a \linkS4class{SingleCellExperiment} object.
133 133
 }
134 134
 \examples{
... ...
@@ -49,19 +49,19 @@ using older versions of \code{celda}.}
49 49
 \item{...}{Ignored. Placeholder to prevent check warning.}
50 50
 
51 51
 \item{useAssay}{A string specifying the name of the
52
-\link[SummarizedExperiment]{assay} slot to use. Default "counts".}
52
+\link{assay} slot to use. Default "counts".}
53 53
 
54
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
54
+\item{altExpName}{The name for the \link{altExp} slot
55 55
 to use. Default "featureSubset".}
56 56
 }
57 57
 \value{
58 58
 A \linkS4class{SingleCellExperiment} object. Function
59
- parameter settings are stored in the \link[S4Vectors]{metadata}
59
+ parameter settings are stored in the \link{metadata}
60 60
  \code{"celda_parameters"} slot.
61 61
  Columns \code{celda_sample_label} and \code{celda_cell_cluster} in
62
- \link[SummarizedExperiment]{colData} contain sample labels and celda cell
62
+ \link{colData} contain sample labels and celda cell
63 63
  population clusters. Column \code{celda_feature_module} in
64
- \link[SummarizedExperiment]{rowData} contain feature modules.
64
+ \link{rowData} contain feature modules.
65 65
 }
66 66
 \description{
67 67
 Convert a old celda model object (\code{celda_C},
... ...
@@ -23,10 +23,10 @@ Rows represent features and columns represent cells.}
23 23
 
24 24
 \item{...}{Ignored. Placeholder to prevent check warning.}
25 25
 
26
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
26
+\item{useAssay}{A string specifying which \link{assay}
27 27
 slot to use. Default "counts".}
28 28
 
29
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
29
+\item{altExpName}{The name for the \link{altExp} slot
30 30
 to use. Default "featureSubset".}
31 31
 
32 32
 \item{log}{Logical. If \code{FALSE}, then the normalized conditional
... ...
@@ -39,11 +39,11 @@ labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a
39 39
 
40 40
 \item{...}{Ignored. Placeholder to prevent check warning.}
41 41
 
42
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
42
+\item{useAssay}{A string specifying which \link{assay}
43 43
 slot to use if \code{x} is a
44 44
 \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".}
45 45
 
46
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
46
+\item{altExpName}{The name for the \link{altExp} slot
47 47
 to use. Default "featureSubset".}
48 48
 
49 49
 \item{c1}{Integer vector. Cell populations to include in group 1 for the
... ...
@@ -40,11 +40,11 @@ counts matrix.}
40 40
 
41 41
 \item{...}{Ignored. Placeholder to prevent check warning.}
42 42
 
43
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
43
+\item{useAssay}{A string specifying which \link{assay}
44 44
 slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.
45 45
 Default "counts".}
46 46
 
47
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
47
+\item{altExpName}{The name for the \link{altExp} slot
48 48
 to use. Default "featureSubset".}
49 49
 
50 50
 \item{type}{Character vector. A vector containing one or more of "counts",
... ...
@@ -25,7 +25,7 @@ Rows represent features and columns represent cells.}
25 25
 \item{feature}{Character vector. Identify feature modules for the specified
26 26
 feature names. \code{feature} must match the rownames of \code{sce}.}
27 27
 
28
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
28
+\item{altExpName}{The name for the \link{altExp} slot
29 29
 to use. Default "featureSubset".}
30 30
 
31 31
 \item{exactMatch}{Logical. Whether to look for exactMatch of the gene name
... ...
@@ -17,10 +17,10 @@ featureModuleTable(
17 17
 located in the \code{useAssay} assay slot.
18 18
 Rows represent features and columns represent cells.}
19 19
 
20
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
20
+\item{useAssay}{A string specifying which \link{assay}
21 21
 slot to use. Default "counts".}
22 22
 
23
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
23
+\item{altExpName}{The name for the \link{altExp} slot
24 24
 to use. Default "featureSubset".}
25 25
 
26 26
 \item{outputFile}{File name for feature module table. If NULL, file will
... ...
@@ -51,11 +51,11 @@ Rows represent features and columns represent cells.}
51 51
 
52 52
 \item{...}{Ignored. Placeholder to prevent check warning.}
53 53
 
54
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
54
+\item{useAssay}{A string specifying which \link{assay}
55 55
 slot to use if \code{x} is a
56 56
 \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".}
57 57
 
58
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
58
+\item{altExpName}{The name for the \link{altExp} slot
59 59
 to use. Default "featureSubset".}
60 60
 
61 61
 \item{class}{Vector of cell cluster labels.}
... ...
@@ -27,11 +27,11 @@ matrix or \linkS4class{SingleCellExperiment} object should be gene names.}
27 27
 
28 28
 \item{...}{Ignored. Placeholder to prevent check warning.}
29 29
 
30
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
30
+\item{useAssay}{A string specifying which \link{assay}
31 31
 slot to use if \code{x} is a
32 32
 \linkS4class{SingleCellExperiment} object. Default "counts".}
33 33
 
34
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
34
+\item{altExpName}{The name for the \link{altExp} slot
35 35
 to use. Default "featureSubset".}
36 36
 
37 37
 \item{databases}{Character vector. Name of reference database. Available
... ...
@@ -29,10 +29,10 @@ Rows represent features and columns represent cells.}
29 29
 
30 30
 \item{...}{Ignored. Placeholder to prevent check warning.}
31 31
 
32
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
32
+\item{useAssay}{A string specifying which \link{assay}
33 33
 slot to use. Default "counts".}
34 34
 
35
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
35
+\item{altExpName}{The name for the \link{altExp} slot
36 36
 to use. Default "featureSubset".}
37 37
 }
38 38
 \value{
... ...
@@ -19,7 +19,7 @@ model object.}
19 19
 
20 20
 \item{...}{Ignored. Placeholder to prevent check warning.}
21 21
 
22
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
22
+\item{altExpName}{The name for the \link{altExp} slot
23 23
 to use. Default "featureSubset".}
24 24
 }
25 25
 \value{
... ...
@@ -46,11 +46,11 @@ Rows represent features and columns represent cells.}
46 46
 
47 47
 \item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.}
48 48
 
49
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
49
+\item{useAssay}{A string specifying which \link{assay}
50 50
 slot to use if \code{x} is a
51 51
 \linkS4class{SingleCellExperiment} object. Default "counts".}
52 52
 
53
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
53
+\item{altExpName}{The name for the \link{altExp} slot
54 54
 to use. Default "featureSubset".}
55 55
 
56 56
 \item{featureModule}{Integer Vector. The featureModule(s) to display.
... ...
@@ -39,11 +39,11 @@ counts matrix.}
39 39
 
40 40
 \item{...}{Ignored. Placeholder to prevent check warning.}
41 41
 
42
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
42
+\item{useAssay}{A string specifying which \link{assay}
43 43
 slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object.
44 44
 Default "counts".}
45 45
 
46
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
46
+\item{altExpName}{The name for the \link{altExp} slot
47 47
 to use. Default "featureSubset".}
48 48
 
49 49
 \item{newCounts}{A new counts matrix used to calculate perplexity. If NULL,
... ...
@@ -36,11 +36,11 @@ represent features and columns represent cells.}
36 36
 
37 37
 \item{features}{Character vector. Uses these genes for plotting.}
38 38
 
39
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
39
+\item{useAssay}{A string specifying which \link{assay}
40 40
 slot to use if \code{x} is a
41 41
 \linkS4class{SingleCellExperiment} object. Default "counts".}
42 42
 
43
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
43
+\item{altExpName}{The name for the \link{altExp} slot
44 44
 to use. Default "featureSubset".}
45 45
 
46 46
 \item{exactMatch}{Logical. Whether an exact match or a partial match using
... ...
@@ -49,7 +49,7 @@ column in \code{colData(x)}.}
49 49
 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and
50 50
 \code{dim2} are set.}
51 51
 
52
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
52
+\item{altExpName}{The name for the \link{altExp} slot
53 53
 to use. Default "featureSubset".}
54 54
 
55 55
 \item{dim1}{Numeric vector. First dimension from data
... ...
@@ -73,11 +73,11 @@ dimension reduction output.}
73 73
 \item{dim2}{Numeric vector. Second dimension from data dimension
74 74
 reduction output.}
75 75
 
76
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
76
+\item{useAssay}{A string specifying which \link{assay}
77 77
 slot to use if \code{x} is a
78 78
 \linkS4class{SingleCellExperiment} object. Default "counts".}
79 79
 
80
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
80
+\item{altExpName}{The name for the \link{altExp} slot
81 81
 to use. Default "featureSubset".}
82 82
 
83 83
 \item{features}{Character vector. Features in the rownames of counts to plot.}
... ...
@@ -99,7 +99,7 @@ and standard deviation of 1. Default \code{TRUE}.}
99 99
 and upper bounds for the data. This threshold is applied after row scaling.
100 100
 Set to NULL to disable. Default \code{c(-1,1)}.}
101 101
 
102
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range
102
+\item{limits}{Passed to \link{scale_colour_gradient2}. The range
103 103
 of color scale.}
104 104
 
105 105
 \item{size}{Numeric. Sets size of point on plot. Default 1.}
... ...
@@ -65,11 +65,11 @@ reduction output.}
65 65
 \item{dim2}{Numeric vector. Second dimension from data dimension
66 66
 reduction output.}
67 67
 
68
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
68
+\item{useAssay}{A string specifying which \link{assay}
69 69
 slot to use if \code{x} is a
70 70
 \linkS4class{SingleCellExperiment} object. Default "counts".}
71 71
 
72
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
72
+\item{altExpName}{The name for the \link{altExp} slot
73 73
 to use. Default "featureSubset".}
74 74
 
75 75
 \item{size}{Numeric. Sets size of point on plot. Default 1.}
... ...
@@ -78,7 +78,7 @@ to use. Default "featureSubset".}
78 78
 
79 79
 \item{ylab}{Character vector. Label for the y-axis. Default 'Dimension_2'.}
80 80
 
81
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range
81
+\item{limits}{Passed to \link{scale_colour_gradient2}. The range
82 82
 of color scale.}
83 83
 
84 84
 \item{colorLow}{Character. A color available from `colors()`.
... ...
@@ -63,11 +63,11 @@ First dimension from data dimension reduction output.}
63 63
 \item{dim2}{Numeric vector.
64 64
 Second dimension from data dimension reduction output.}
65 65
 
66
-\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay}
66
+\item{useAssay}{A string specifying which \link{assay}
67 67
 slot to use if \code{x} is a
68 68
 \linkS4class{SingleCellExperiment} object. Default "counts".}
69 69
 
70
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
70
+\item{altExpName}{The name for the \link{altExp} slot
71 71
 to use. Default "featureSubset".}
72 72
 
73 73
 \item{modules}{Character vector. Module(s) from celda model to be plotted.
... ...
@@ -76,7 +76,7 @@ e.g. c("1", "2").}
76 76
 \item{rescale}{Logical.
77 77
 Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.}
78 78
 
79
-\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient}. The range
79
+\item{limits}{Passed to \link{scale_colour_gradient}. The range
80 80
 of color scale.}
81 81
 
82 82
 \item{size}{Numeric. Sets size of point on plot. Default 1.}
... ...
@@ -23,7 +23,7 @@ plotGridSearchPerplexity(x, ...)
23 23
 
24 24
 \item{...}{Ignored. Placeholder to prevent check warning.}
25 25
 
26
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
26
+\item{altExpName}{The name for the \link{altExp} slot
27 27
 to use. Default "featureSubset".}
28 28
 
29 29
 \item{sep}{Numeric. Breaks in the x axis of the resulting plot.}
... ...
@@ -23,7 +23,7 @@ plotGridSearchPerplexityDiff(x, ...)
23 23
 
24 24
 \item{...}{Ignored. Placeholder to prevent check warning.}
25 25
 
26
-\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot
26
+\item{altExpName}{The name for the \link{altExp} slot
27 27
 to use. Defau