From b8f36492951955069be97fb458bef93a8734325d Mon Sep 17 00:00:00 2001 From: zhewa Date: Fri, 16 Oct 2020 10:44:07 -0400 Subject: [PATCH 1/2] update doc --- R/plot_dr.R | 5 ++++- man/plotDimReduceCluster.Rd | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/plot_dr.R b/R/plot_dr.R index 27c43c51..3655d6d4 100755 --- a/R/plot_dr.R +++ b/R/plot_dr.R @@ -802,7 +802,10 @@ setMethod("plotDimReduceModule", #' @description Create a scatterplot for each row of a normalized #' gene expression matrix where x and y axis are from a #' data dimension reduction tool. -#' The cells are colored by its given \code{cluster} label. +#' The cells are colored by "celda_cell_cluster" column in +#' \code{colData(altExp(x, altExpName))} if \code{x} is a +#' \linkS4class{SingleCellExperiment} object, or \code{x} if \code{x} is +#' a integer vector of cell cluster labels. #' @param x Integer vector of cell cluster labels or a #' \linkS4class{SingleCellExperiment} object #' containing cluster labels for each cell in \code{"celda_cell_cluster"} diff --git a/man/plotDimReduceCluster.Rd b/man/plotDimReduceCluster.Rd index 02374099..2124a739 100644 --- a/man/plotDimReduceCluster.Rd +++ b/man/plotDimReduceCluster.Rd @@ -85,7 +85,10 @@ The plot as a ggplot object Create a scatterplot for each row of a normalized gene expression matrix where x and y axis are from a data dimension reduction tool. - The cells are colored by its given \code{cluster} label. + The cells are colored by "celda_cell_cluster" column in + \code{colData(altExp(x, altExpName))} if \code{x} is a + \linkS4class{SingleCellExperiment} object, or \code{x} if \code{x} is + a integer vector of cell cluster labels. } \examples{ data(sceCeldaCG) From 82cc7a6a012aa43af0c8f603333a3a93be12f7e8 Mon Sep 17 00:00:00 2001 From: zhewa Date: Fri, 16 Oct 2020 17:36:32 -0400 Subject: [PATCH 2/2] fix doc warning file link in package does not exist and so has been treated as a topic --- DESCRIPTION | 2 +- R/accessors.R | 14 +++++------ R/celdaGridSearch.R | 18 +++++++------- R/celdaProbabilityMap.R | 4 ++-- R/celdaUMAP.R | 6 ++--- R/celda_C.R | 14 +++++------ R/celda_CG.R | 37 +++++++++++++++-------------- R/celda_G.R | 14 +++++------ R/celda_functions.R | 12 +++++----- R/celda_heatmap.R | 4 ++-- R/celdatSNE.R | 6 ++--- R/celdatosce.R | 10 ++++---- R/clusterProbability.R | 4 ++-- R/diffExp.R | 4 ++-- R/factorizeMatrix.R | 4 ++-- R/featureModuleLookup.R | 2 +- R/findMarkersTree.R | 4 ++-- R/geneSetEnrich.R | 4 ++-- R/loglikelihood.R | 8 +++---- R/moduleHeatmap.R | 4 ++-- R/perplexity.R | 12 +++++----- R/plot_dr.R | 24 +++++++++---------- R/recursiveSplit.R | 12 +++++----- R/selectFeatures.R | 12 +++++----- R/simulateCells.R | 6 ++--- R/splitModule.R | 6 ++--- man/bestLogLikelihood.Rd | 2 +- man/celdaClusters.Rd | 4 ++-- man/celdaGridSearch.Rd | 6 ++--- man/celdaHeatmap.Rd | 4 ++-- man/celdaModel.Rd | 2 +- man/celdaModules.Rd | 2 +- man/celdaProbabilityMap.Rd | 4 ++-- man/celdaTsne.Rd | 6 ++--- man/celdaUmap.Rd | 6 ++--- man/celda_C.Rd | 14 +++++------ man/celda_CG.Rd | 37 +++++++++++++++-------------- man/celda_G.Rd | 14 +++++------ man/celdatosce.Rd | 10 ++++---- man/clusterProbability.Rd | 4 ++-- man/differentialExpression.Rd | 4 ++-- man/factorizeMatrix.Rd | 4 ++-- man/featureModuleLookup.Rd | 2 +- man/featureModuleTable.Rd | 4 ++-- man/findMarkersTree.Rd | 4 ++-- man/geneSetEnrich.Rd | 4 ++-- man/logLikelihood.Rd | 4 ++-- man/logLikelihoodHistory.Rd | 2 +- man/moduleHeatmap.Rd | 4 ++-- man/perplexity.Rd | 4 ++-- man/plotCeldaViolin.Rd | 4 ++-- man/plotDimReduceCluster.Rd | 2 +- man/plotDimReduceFeature.Rd | 6 ++--- man/plotDimReduceGrid.Rd | 6 ++--- man/plotDimReduceModule.Rd | 6 ++--- man/plotGridSearchPerplexity.Rd | 2 +- man/plotGridSearchPerplexityDiff.Rd | 2 +- man/recodeClusterY.Rd | 4 ++-- man/recodeClusterZ.Rd | 4 ++-- man/recursiveSplitCell.Rd | 6 ++--- man/recursiveSplitModule.Rd | 6 ++--- man/resList.Rd | 2 +- man/resamplePerplexity.Rd | 4 ++-- man/runParams.Rd | 2 +- man/sampleLabel.Rd | 2 +- man/selectBestModel.Rd | 6 ++--- man/selectFeatures.Rd | 12 +++++----- man/simulateCells.Rd | 6 ++--- man/splitModule.Rd | 6 ++--- man/subsetCeldaList.Rd | 6 ++--- 70 files changed, 247 insertions(+), 245 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a4a4f519..73e3a4db 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: celda Title: CEllular Latent Dirichlet Allocation -Version: 1.5.10 +Version: 1.5.11 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", role = c("aut", "cre")), person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")), diff --git a/R/accessors.R b/R/accessors.R index db40e0d1..dc5f409e 100644 --- a/R/accessors.R +++ b/R/accessors.R @@ -8,10 +8,10 @@ #' \item A \linkS4class{SingleCellExperiment} object returned by #' \link{celda_C}, or \link{celda_CG}, with the matrix #' located in the \code{useAssay} assay slot. The -#' a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will +#' a \link{altExp} slot with name \code{altExpName} will #' be used. Rows represent features and columns represent cells. #' \item Celda model object.} -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param value Character vector of cell cluster labels for replacements. Works #' only if \code{x} is a \linkS4class{SingleCellExperiment} object. @@ -85,7 +85,7 @@ setReplaceMethod("celdaClusters", signature(x = "SingleCellExperiment"), #' \link{celda_G}, or \link{celda_CG}, with the matrix #' located in the \code{useAssay} assay slot. #' Rows represent features and columns represent cells. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param value Character vector of feature module labels for replacements. #' Works only if \code{x} is a \linkS4class{SingleCellExperiment} object. @@ -141,7 +141,7 @@ setReplaceMethod("celdaModules", signature(sce = "SingleCellExperiment"), #' located in the \code{useAssay} assay slot. #' Rows represent features and columns represent cells. #' \item A celda model object.} -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param value Character vector of sample labels for replacements. Works #' only is \code{x} is a \linkS4class{SingleCellExperiment} object. @@ -263,7 +263,7 @@ setMethod("matrixNames", #' priors from the celdaList object when it was created. #' @param x An object of class \linkS4class{SingleCellExperiment} or class #' \code{celdaList}. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return Data Frame. Contains details on the various K/L parameters, chain @@ -310,7 +310,7 @@ setMethod("runParams", #' \link{celdaGridSearch} run. #' @param x An object of class \linkS4class{SingleCellExperiment} or #' \code{celdaList}. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return List. Contains one celdaModel object for each of the parameters @@ -357,7 +357,7 @@ setMethod("resList", #' \link{celda_C}, \link{celda_G} or \link{celda_CG}. #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return Character. The celda model. Can be one of "celda_C", "celda_G", or diff --git a/R/celdaGridSearch.R b/R/celdaGridSearch.R index 4d2329cd..90f01151 100755 --- a/R/celdaGridSearch.R +++ b/R/celdaGridSearch.R @@ -12,8 +12,8 @@ #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param model Celda model. Options available in \link{availableModels}. #' @param paramsTest List. A list denoting the combinations of parameters to @@ -45,7 +45,7 @@ #' and main process. Default "Celda". #' @return A \linkS4class{SingleCellExperiment} object. Function #' parameter settings and celda model results are stored in the -#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. +#' \link{metadata} \code{"celda_grid_search"} slot. #' @param ... Ignored. Placeholder to prevent check warning. #' @seealso \link{celda_G} for feature clustering, \link{celda_C} for #' clustering of cells, and \link{celda_CG} for simultaneous clustering of @@ -440,7 +440,7 @@ setMethod("celdaGridSearch", #' \item celdaList object.} #' @param params List. List of parameters used to subset the matching celda #' models in list \code{"celda_grid_search"} in \code{metadata(x)}. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return One of @@ -451,10 +451,10 @@ setMethod("celdaGridSearch", #' \code{"celda_grid_search"} slot in \code{metadata(x)} matches #' the given criteria, a new \linkS4class{SingleCellExperiment} object #' with the matching model stored in the -#' \link[S4Vectors]{metadata} +#' \link{metadata} #' \code{"celda_parameters"} slot will be returned. Otherwise, a new #' \linkS4class{SingleCellExperiment} object with the subset models stored -#' in the \link[S4Vectors]{metadata} +#' in the \link{metadata} #' \code{"celda_grid_search"} slot will be returned. #' \item A new \code{celdaList} object containing all models matching the #' provided criteria in \code{params}. If only one item in the @@ -581,7 +581,7 @@ setMethod("subsetCeldaList", #' best model as a #' \code{celdaList} object or not. If \code{FALSE}, return the best model as a #' corresponding celda model object. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return One of @@ -591,10 +591,10 @@ setMethod("subsetCeldaList", #' \code{metadata(x)}. If there is only one set of parameters, #' a new \linkS4class{SingleCellExperiment} object #' with the matching model stored in the -#' \link[S4Vectors]{metadata} +#' \link{metadata} #' \code{"celda_parameters"} slot will be returned. Otherwise, a new #' \linkS4class{SingleCellExperiment} object with the subset models stored -#' in the \link[S4Vectors]{metadata} +#' in the \link{metadata} #' \code{"celda_grid_search"} slot will be returned. #' \item A new \code{celdaList} object containing one model with the best #' log-likelihood for each set of parameters. If only one set of parameters diff --git a/R/celdaProbabilityMap.R b/R/celdaProbabilityMap.R index 66696353..99edbe93 100644 --- a/R/celdaProbabilityMap.R +++ b/R/celdaProbabilityMap.R @@ -4,9 +4,9 @@ #' populations and samples). #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param level Character. One of "cellPopulation" or "Sample". #' "cellPopulation" will display the absolute probabilities and relative diff --git a/R/celdaUMAP.R b/R/celdaUMAP.R index 83bc0d47..472409cb 100644 --- a/R/celdaUMAP.R +++ b/R/celdaUMAP.R @@ -8,9 +8,9 @@ #' transformed before applying UMAP. #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param maxCells Integer. Maximum number of cells to plot. Cells will be #' randomly subsampled if \code{ncol(sce) > maxCells}. Larger numbers of cells @@ -62,7 +62,7 @@ #' @param ... Additional parameters to pass to \link[uwot]{umap}. #' @return \code{sce} with UMAP coordinates #' (columns "celda_UMAP1" & "celda_UMAP2") added to -#' \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}. +#' \code{\link{reducedDim}(sce, "celda_UMAP")}. #' @export setGeneric("celdaUmap", function(sce, ...) { diff --git a/R/celda_C.R b/R/celda_C.R index cf6c1106..3ff0465b 100755 --- a/R/celda_C.R +++ b/R/celda_C.R @@ -1,10 +1,10 @@ #' @title Cell clustering with Celda #' @description Clusters the columns of a count matrix containing single-cell #' data into K subpopulations. The -#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in -#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if +#' \code{useAssay} \link{assay} slot in +#' \code{altExpName} \link{altExp} slot will be used if #' it exists. Otherwise, the \code{useAssay} -#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if +#' \link{assay} slot in \code{x} will be used if #' \code{x} is a \linkS4class{SingleCellExperiment} object. #' @param x A numeric \link{matrix} of counts or a #' \linkS4class{SingleCellExperiment} @@ -12,8 +12,8 @@ #' \code{altExp(x, altExpName)}. #' Rows represent features and columns represent cells. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param sampleLabel Vector or factor. Denotes the sample label for each cell #' (column) in the count matrix. @@ -59,10 +59,10 @@ #' @param verbose Logical. Whether to print log messages. Default TRUE. #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object. Function -#' parameter settings are stored in the \link[S4Vectors]{metadata} +#' parameter settings are stored in the \link{metadata} #' \code{"celda_parameters"} slot. #' Columns \code{celda_sample_label} and \code{celda_cell_cluster} in -#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell +#' \link{colData} contain sample labels and celda cell #' population clusters. #' @seealso \link{celda_G} for feature clustering and \link{celda_CG} for #' simultaneous clustering of features and cells. \link{celdaGridSearch} can diff --git a/R/celda_CG.R b/R/celda_CG.R index 35c2bba7..5b8965e7 100755 --- a/R/celda_CG.R +++ b/R/celda_CG.R @@ -1,19 +1,19 @@ #' @title Cell and feature clustering with Celda #' @description Clusters the rows and columns of a count matrix containing #' single-cell data into L modules and K subpopulations, respectively. The -#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in -#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if +#' \code{useAssay} \link{assay} slot in +#' \code{altExpName} \link{altExp} slot will be used if #' it exists. Otherwise, the \code{useAssay} -#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if +#' \link{assay} slot in \code{x} will be used if #' \code{x} is a \linkS4class{SingleCellExperiment} object. #' @param x A numeric \link{matrix} of counts or a #' \linkS4class{SingleCellExperiment} -#' with the matrix located in the \link[SummarizedExperiment]{assay} +#' with the matrix located in the \link{assay} #' slot under \code{useAssay} in \code{altExp(x, altExpName)}. #' Rows represent features and columns represent cells. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param sampleLabel Vector or factor. Denotes the sample label for each cell #' (column) in the count matrix. @@ -35,11 +35,12 @@ #' likelihood to stop inference. Default 10. #' @param maxIter Integer. Maximum number of iterations of Gibbs sampling to #' perform. Default 200. -#' @param splitOnIter Integer. On every `splitOnIter` iteration, a heuristic +#' @param splitOnIter Integer. On every \code{splitOnIter} iteration, +#' a heuristic #' will be applied to determine if a cell population or feature module should #' be reassigned and another cell population or feature module should be split #' into two clusters. To disable splitting, set to -1. Default 10. -#' @param splitOnLast Integer. After `stopIter` iterations have been +#' @param splitOnLast Integer. After \code{stopIter} iterations have been #' performed without improvement, a heuristic will be applied to determine if #' a cell population or feature module should be reassigned and another cell #' population or feature module should be split into two clusters. If a split @@ -52,32 +53,32 @@ #' With 'random', cells are randomly assigned to a populations. With 'split', #' cells will be split into sqrt(K) populations and then each popluation will #' be subsequently split into another sqrt(K) populations. With 'predefined', -#' values in `zInit` will be used to initialize `z`. Default 'split'. +#' values in \code{zInit} will be used to initialize \code{z}. Default 'split'. #' @param yInitialize Chararacter. One of 'random', 'split', or 'predefined'. #' With 'random', features are randomly assigned to a modules. With 'split', #' features will be split into sqrt(L) modules and then each module will be #' subsequently split into another sqrt(L) modules. With 'predefined', values -#' in `yInit` will be used to initialize `y`. Default 'split'. +#' in \code{yInit} will be used to initialize \code{y}. Default 'split'. #' @param zInit Integer vector. Sets initial starting values of z. If NULL, #' starting values for each cell will be randomly sampled from 1:K. 'zInit' -#' can only be used when `initialize' = 'random'`. Default NULL. +#' can only be used when \code{initialize = "random"}. Default NULL. #' @param yInit Integer vector. Sets initial starting values of y. If NULL, #' starting values for each feature will be randomly sampled from 1:L. -#' 'yInit' can only be used when `initialize = 'random'`. Default NULL. -#' @param countChecksum Character. An MD5 checksum for the `counts` matrix. +#' 'yInit' can only be used when \code{initialize = "random"}. Default NULL. +#' @param countChecksum Character. An MD5 checksum for the counts matrix. #' Default NULL. #' @param logfile Character. Messages will be redirected to a file named #' `logfile`. If NULL, messages will be printed to stdout. Default NULL. #' @param verbose Logical. Whether to print log messages. Default TRUE. #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object. Function -#' parameter settings are stored in \link[S4Vectors]{metadata} -#' \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot. -#' In \link[SingleCellExperiment]{altExp} slot, +#' parameter settings are stored in \link{metadata} +#' \code{"celda_parameters"} in \link{altExp} slot. +#' In \link{altExp} slot, #' columns \code{celda_sample_label} and \code{celda_cell_cluster} in -#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell +#' \link{colData} contain sample labels and celda cell #' population clusters. Column \code{celda_feature_module} in -#' \link[SummarizedExperiment]{rowData} contains feature modules. +#' \link{rowData} contains feature modules. #' @seealso \link{celda_G} for feature clustering and \link{celda_C} for #' clustering cells. \link{celdaGridSearch} can be used to run multiple #' values of K/L and multiple chains in parallel. diff --git a/R/celda_G.R b/R/celda_G.R index 5508dabc..34d0ad6a 100755 --- a/R/celda_G.R +++ b/R/celda_G.R @@ -1,18 +1,18 @@ #' @title Feature clustering with Celda #' @description Clusters the rows of a count matrix containing single-cell data #' into L modules. The -#' \code{useAssay} \link[SummarizedExperiment]{assay} slot in -#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if +#' \code{useAssay} \link{assay} slot in +#' \code{altExpName} \link{altExp} slot will be used if #' it exists. Otherwise, the \code{useAssay} -#' \link[SummarizedExperiment]{assay} slot in \code{x} will be used if +#' \link{assay} slot in \code{x} will be used if #' \code{x} is a \linkS4class{SingleCellExperiment} object. #' @param x A numeric \link{matrix} of counts or a #' \linkS4class{SingleCellExperiment} #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param L Integer. Number of feature modules. #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to @@ -53,9 +53,9 @@ #' @param verbose Logical. Whether to print log messages. Default TRUE. #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object. Function -#' parameter settings are stored in the \link[S4Vectors]{metadata} +#' parameter settings are stored in the \link{metadata} #' \code{"celda_parameters"} slot. Column \code{celda_feature_module} in -#' \link[SummarizedExperiment]{rowData} contains feature modules. +#' \link{rowData} contains feature modules. #' @seealso \link{celda_C} for cell clustering and \link{celda_CG} for #' simultaneous clustering of features and cells. \link{celdaGridSearch} can #' be used to run multiple values of L and multiple chains in parallel. diff --git a/R/celda_functions.R b/R/celda_functions.R index b590a094..f7b5282b 100755 --- a/R/celda_functions.R +++ b/R/celda_functions.R @@ -137,7 +137,7 @@ normalizeCounts <- function(counts, #' @param sce \linkS4class{SingleCellExperiment} object returned from #' \link{celda_C} or \link{celda_CG}. Must contain column #' \code{celda_cell_cluster} in -#' \code{\link[SummarizedExperiment]{colData}(altExp(sce, altExpName))}. +#' \code{\link{colData}(altExp(sce, altExpName))}. #' @param from Numeric vector. Unique values in the range of #' \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to #' the original cluster @@ -145,7 +145,7 @@ normalizeCounts <- function(counts, #' @param to Numeric vector. Unique values in the range of #' \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to #' the new cluster labels. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @return \linkS4class{SingleCellExperiment} object with recoded cell #' cluster labels. @@ -188,13 +188,13 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") { #' @param sce \linkS4class{SingleCellExperiment} object returned from #' \link{celda_G} or \link{celda_CG}. Must contain column #' \code{celda_feature_module} in -#' \code{\link[SummarizedExperiment]{rowData}(altExp(sce, altExpName))}. +#' \code{\link{rowData}(altExp(sce, altExpName))}. #' @param from Numeric vector. Unique values in the range of #' \code{seq(celdaModules(sce))} that correspond to the original module labels #' in \code{sce}. #' @param to Numeric vector. Unique values in the range of #' \code{seq(celdaModules(sce))} that correspond to the new module labels. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @return @return \linkS4class{SingleCellExperiment} object with recoded #' feature module labels. @@ -525,9 +525,9 @@ distinctColors <- function(n, #' \link{celda_G}, or \link{celda_CG}, with the matrix #' located in the \code{useAssay} assay slot. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param outputFile File name for feature module table. If NULL, file will #' not be created. Default NULL. diff --git a/R/celda_heatmap.R b/R/celda_heatmap.R index 528467cb..b9cb3508 100644 --- a/R/celda_heatmap.R +++ b/R/celda_heatmap.R @@ -3,9 +3,9 @@ #' clustering results. #' @param sce A \link[SingleCellExperiment]{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param featureIx Integer vector. Select features for display in heatmap. If #' NULL, no subsetting will be performed. Default NULL. \strong{Only used for diff --git a/R/celdatSNE.R b/R/celdatSNE.R index 2c447293..6e87460e 100644 --- a/R/celdatSNE.R +++ b/R/celdatSNE.R @@ -8,9 +8,9 @@ #' Module probabilities are square-root transformed before applying tSNE. #' @param sce A \linkS4class{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param maxCells Integer. Maximum number of cells to plot. Cells will be #' randomly subsampled if \code{ncol(counts) > maxCells}. Larger numbers of @@ -48,7 +48,7 @@ #' @param ... Ignored. Placeholder to prevent check warning. #' @return \code{sce} with t-SNE coordinates #' (columns "celda_tSNE1" & "celda_tSNE2") added to -#' \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}. +#' \code{\link{reducedDim}(sce, "celda_tSNE")}. #' @export setGeneric("celdaTsne", function(sce, ...) { diff --git a/R/celdatosce.R b/R/celdatosce.R index f29ec8d6..f566ecf1 100644 --- a/R/celdatosce.R +++ b/R/celdatosce.R @@ -11,17 +11,17 @@ #' \code{celdaModel}. Dimensions and MD5 checksum will be checked by #' \link{compareCountMatrix}. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object. Function -#' parameter settings are stored in the \link[S4Vectors]{metadata} +#' parameter settings are stored in the \link{metadata} #' \code{"celda_parameters"} slot. #' Columns \code{celda_sample_label} and \code{celda_cell_cluster} in -#' \link[SummarizedExperiment]{colData} contain sample labels and celda cell +#' \link{colData} contain sample labels and celda cell #' population clusters. Column \code{celda_feature_module} in -#' \link[SummarizedExperiment]{rowData} contain feature modules. +#' \link{rowData} contain feature modules. #' @export setGeneric("celdatosce", function(celdaModel, counts, ...) { standardGeneric("celdatosce")}) diff --git a/R/clusterProbability.R b/R/clusterProbability.R index 63537674..674b12cc 100644 --- a/R/clusterProbability.R +++ b/R/clusterProbability.R @@ -8,9 +8,9 @@ #' \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix #' located in the \code{useAssay} assay slot. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param log Logical. If \code{FALSE}, then the normalized conditional #' probabilities will be returned. If \code{TRUE}, then the unnormalized log diff --git a/R/diffExp.R b/R/diffExp.R index 4c5fc53b..84bba179 100755 --- a/R/diffExp.R +++ b/R/diffExp.R @@ -7,10 +7,10 @@ #' Rows represent features and columns represent cells. Must contain cluster #' labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a #' \linkS4class{SingleCellExperiment} object. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod Celda object of class `celda_C` or `celda_CG`. #' @param c1 Integer vector. Cell populations to include in group 1 for the diff --git a/R/factorizeMatrix.R b/R/factorizeMatrix.R index dfa17b2a..f35bdf6e 100644 --- a/R/factorizeMatrix.R +++ b/R/factorizeMatrix.R @@ -11,10 +11,10 @@ #' \item Integer counts matrix. Rows represent features and columns represent #' cells. This matrix should be the same as the one used to generate #' \code{celdaMod}.} -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. #' Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod Celda model object. Only works if \code{x} is an integer #' counts matrix. diff --git a/R/featureModuleLookup.R b/R/featureModuleLookup.R index f3a51dda..a216f839 100644 --- a/R/featureModuleLookup.R +++ b/R/featureModuleLookup.R @@ -8,7 +8,7 @@ #' Rows represent features and columns represent cells. #' @param feature Character vector. Identify feature modules for the specified #' feature names. \code{feature} must match the rownames of \code{sce}. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param exactMatch Logical. Whether to look for exactMatch of the gene name #' within counts matrix. Default \code{TRUE}. diff --git a/R/findMarkersTree.R b/R/findMarkersTree.R index 179bcf64..6ac86a8a 100644 --- a/R/findMarkersTree.R +++ b/R/findMarkersTree.R @@ -9,10 +9,10 @@ #' \linkS4class{SingleCellExperiment} #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param class Vector of cell cluster labels. #' @param oneoffMetric A character string. What one-off metric to run, either diff --git a/R/geneSetEnrich.R b/R/geneSetEnrich.R index e8e71080..a48d1cd1 100644 --- a/R/geneSetEnrich.R +++ b/R/geneSetEnrich.R @@ -9,10 +9,10 @@ #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. Rownames of the #' matrix or \linkS4class{SingleCellExperiment} object should be gene names. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaModel Celda object of class \code{celda_G} or \code{celda_CG}. #' @param databases Character vector. Name of reference database. Available diff --git a/R/loglikelihood.R b/R/loglikelihood.R index 43c0cfc0..72cb49ba 100644 --- a/R/loglikelihood.R +++ b/R/loglikelihood.R @@ -5,9 +5,9 @@ #' \link{celda_C}, \link{celda_G}, or \link{celda_CG}, with the matrix #' located in the \code{useAssay} assay slot. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod celda model object. Ignored if \code{x} is a #' \linkS4class{SingleCellExperiment} object. @@ -154,7 +154,7 @@ setMethod("logLikelihood", signature(x = "matrix", celdaMod = "celda_CG"), #' @param x A \linkS4class{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda #' model object. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return Numeric. The log-likelihood at each step of Gibbs sampling used to @@ -205,7 +205,7 @@ setMethod("logLikelihoodHistory", #' @param x A \linkS4class{SingleCellExperiment} object #' returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}, or a celda #' model object. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @export diff --git a/R/moduleHeatmap.R b/R/moduleHeatmap.R index a5a8f9f3..37b89ef2 100644 --- a/R/moduleHeatmap.R +++ b/R/moduleHeatmap.R @@ -10,10 +10,10 @@ #' \linkS4class{SingleCellExperiment} #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param featureModule Integer Vector. The featureModule(s) to display. #' Multiple modules can be included in a vector. Default \code{NULL} which diff --git a/R/perplexity.R b/R/perplexity.R index f542d292..bebdf023 100644 --- a/R/perplexity.R +++ b/R/perplexity.R @@ -10,10 +10,10 @@ #' \item Integer counts matrix. Rows represent features and columns represent #' cells. This matrix should be the same as the one used to generate #' \code{celdaMod}.} -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. #' Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod Celda model object. Only works if \code{x} is an integer #' counts matrix. @@ -347,10 +347,10 @@ setMethod( #' Rows represent features and columns represent cells. Must contain #' "celda_grid_search" slot in \code{metadata(x)} if \code{x} is a #' \linkS4class{SingleCellExperiment} object. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaList Object of class 'celdaList'. Used only if \code{x} is a #' matrix object. @@ -483,7 +483,7 @@ setMethod("resamplePerplexity", #' or \code{recursiveSplitCell}. Must contain a list named #' \code{"celda_grid_search"} in \code{metadata(x)}. #' \item celdaList object.} -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param sep Numeric. Breaks in the x axis of the resulting plot. #' @param ... Ignored. Placeholder to prevent check warning. @@ -743,7 +743,7 @@ setMethod("plotGridSearchPerplexity", #' or \code{recursiveSplitCell}. Must contain a list named #' \code{"celda_grid_search"} in \code{metadata(x)}. #' \item celdaList object.} -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param sep Numeric. Breaks in the x axis of the resulting plot. #' @param n Integer. Width of the rolling window. Default 10. diff --git a/R/plot_dr.R b/R/plot_dr.R index 3655d6d4..43bc425c 100755 --- a/R/plot_dr.R +++ b/R/plot_dr.R @@ -12,15 +12,15 @@ #' reduction output. #' @param dim2 Numeric vector. Second dimension from data dimension #' reduction output. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param size Numeric. Sets size of point on plot. Default 1. #' @param xlab Character vector. Label for the x-axis. Default 'Dimension_1'. #' @param ylab Character vector. Label for the y-axis. Default 'Dimension_2'. -#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range +#' @param limits Passed to \link{scale_colour_gradient2}. The range #' of color scale. #' @param colorLow Character. A color available from `colors()`. #' The color will be used to signify the lowest values on the scale. @@ -291,10 +291,10 @@ setMethod("plotDimReduceGrid", #' dimension reduction output. #' @param dim2 Numeric vector. Second dimension from data dimension #' reduction output. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param features Character vector. Features in the rownames of counts to plot. #' @param headers Character vector. If `NULL`, the corresponding rownames are @@ -309,7 +309,7 @@ setMethod("plotDimReduceGrid", #' @param trim Numeric vector. Vector of length two that specifies the lower #' and upper bounds for the data. This threshold is applied after row scaling. #' Set to NULL to disable. Default \code{c(-1,1)}. -#' @param limits Passed to \link[ggplot2]{scale_colour_gradient2}. The range +#' @param limits Passed to \link{scale_colour_gradient2}. The range #' of color scale. #' @param size Numeric. Sets size of point on plot. Default 1. #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1". @@ -576,10 +576,10 @@ setMethod("plotDimReduceFeature", #' First dimension from data dimension reduction output. #' @param dim2 Numeric vector. #' Second dimension from data dimension reduction output. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if #' \code{x} is a matrix object. @@ -587,7 +587,7 @@ setMethod("plotDimReduceFeature", #' e.g. c("1", "2"). #' @param rescale Logical. #' Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE. -#' @param limits Passed to \link[ggplot2]{scale_colour_gradient}. The range +#' @param limits Passed to \link{scale_colour_gradient}. The range #' of color scale. #' @param size Numeric. Sets size of point on plot. Default 1. #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1". @@ -814,7 +814,7 @@ setMethod("plotDimReduceModule", #' \code{reducedDimNames(x)} if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and #' \code{dim2} are set. -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param dim1 Numeric vector. First dimension from data #' dimension reduction output. @@ -1027,10 +1027,10 @@ setMethod("plotDimReduceCluster", #' with the matrix located in the assay slot under \code{useAssay}. Rows #' represent features and columns represent cells. #' @param features Character vector. Uses these genes for plotting. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \linkS4class{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param celdaMod Celda object of class "celda_G" or "celda_CG". Used only if #' \code{x} is a matrix object. diff --git a/R/recursiveSplit.R b/R/recursiveSplit.R index 3ea86b53..d509e51e 100644 --- a/R/recursiveSplit.R +++ b/R/recursiveSplit.R @@ -90,9 +90,9 @@ #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} +#' \link{assay} #' slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param sampleLabel Vector or factor. Denotes the sample label for each cell #' (column) in the count matrix. @@ -137,7 +137,7 @@ #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object. Function #' parameter settings and celda model results are stored in the -#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in +#' \link{metadata} \code{"celda_grid_search"} slot. The models in #' the list will be of class \code{celda_C} if \code{yInit = NULL} or #' \code{celda_CG} if \code{zInit} is set. #' @seealso \link{recursiveSplitModule} for recursive splitting of feature @@ -859,10 +859,10 @@ setMethod("recursiveSplitCell", #' \linkS4class{SingleCellExperiment} #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use if \code{x} is a #' \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param initialL Integer. Minimum number of modules to try. #' @param maxL Integer. Maximum number of modules to try. @@ -905,7 +905,7 @@ setMethod("recursiveSplitCell", #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object. Function #' parameter settings and celda model results are stored in the -#' \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in +#' \link{metadata} \code{"celda_grid_search"} slot. The models in #' the list will be of class \link{celda_G} if \code{zInit = NULL} or #' \link{celda_CG} if \code{zInit} is set. #' @seealso \code{recursiveSplitCell} for recursive splitting of cell diff --git a/R/selectFeatures.R b/R/selectFeatures.R index bb007814..c8f64898 100644 --- a/R/selectFeatures.R +++ b/R/selectFeatures.R @@ -3,8 +3,8 @@ #' Select features with at least \code{minCount} counts #' in at least \code{minCell} cells. A \linkS4class{SingleCellExperiment} #' object with subset features will be stored in the -#' \link[SingleCellExperiment]{altExp} slot with name \code{altExpName}. -#' The name of the \code{assay} slot in \link[SingleCellExperiment]{altExp} +#' \link{altExp} slot with name \code{altExpName}. +#' The name of the \code{assay} slot in \link{altExp} #' will be the same as \code{useAssay}. #' @param x A numeric \link{matrix} of counts or a #' \linkS4class{SingleCellExperiment} @@ -13,13 +13,13 @@ #' @param minCount Minimum number of counts required for feature selection. #' @param minCell Minimum number of cells required for feature selection. #' @param useAssay A string specifying the name of the -#' \link[SummarizedExperiment]{assay} slot to use. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' \link{assay} slot to use. Default "counts". +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param ... Ignored. Placeholder to prevent check warning. #' @return A \linkS4class{SingleCellExperiment} object with a -#' \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function -#' parameter settings are stored in the \link[S4Vectors]{metadata} +#' \code{altExpName} \link{altExp} slot. Function +#' parameter settings are stored in the \link{metadata} #' \code{"select_features"} slot. #' @export setGeneric("selectFeatures", function(x, ...) { diff --git a/R/simulateCells.R b/R/simulateCells.R index db24f766..dc6c3836 100644 --- a/R/simulateCells.R +++ b/R/simulateCells.R @@ -41,13 +41,13 @@ #' \link[withr]{with_seed} are made. #' @return A \link[SingleCellExperiment]{SingleCellExperiment} object with #' simulated count matrix stored in the "counts" assay slot. Function -#' parameter settings are stored in the \link[S4Vectors]{metadata} slot. For +#' parameter settings are stored in the \link{metadata} slot. For #' \code{"celda_CG"} and \code{"celda_C"} models, #' columns \code{celda_sample_label} and \code{celda_cell_cluster} in -#' \link[SummarizedExperiment]{colData} contain simulated sample labels and +#' \link{colData} contain simulated sample labels and #' cell population clusters. For \code{"celda_CG"} and \code{"celda_G"} #' models, column \code{celda_feature_module} in -#' \link[SummarizedExperiment]{rowData} contains simulated gene modules. +#' \link{rowData} contains simulated gene modules. #' @examples #' sce <- simulateCells() #' @export diff --git a/R/splitModule.R b/R/splitModule.R index 943bac32..a3d46874 100644 --- a/R/splitModule.R +++ b/R/splitModule.R @@ -5,9 +5,9 @@ #' @param x A \linkS4class{SingleCellExperiment} object #' with the matrix located in the assay slot under \code{useAssay}. #' Rows represent features and columns represent cells. -#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay} +#' @param useAssay A string specifying which \link{assay} #' slot to use for \code{x}. Default "counts". -#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot +#' @param altExpName The name for the \link{altExp} slot #' to use. Default "featureSubset". #' @param module Integer. The module to be split. #' @param n Integer. How many modules should \code{module} be split into. @@ -18,7 +18,7 @@ #' @param ... Ignored. Placeholder to prevent check warning. #' @return A updated \linkS4class{SingleCellExperiment} object with new #' feature modules stored in column \code{celda_feature_module} in -#' \code{\link[SummarizedExperiment]{rowData}(x)}. +#' \code{\link{rowData}(x)}. #' @export setGeneric("splitModule", function(x, ...) { diff --git a/man/bestLogLikelihood.Rd b/man/bestLogLikelihood.Rd index 88634dce..15d4cb1a 100644 --- a/man/bestLogLikelihood.Rd +++ b/man/bestLogLikelihood.Rd @@ -19,7 +19,7 @@ model object.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/celdaClusters.Rd b/man/celdaClusters.Rd index 8b6639f0..9f06ba44 100644 --- a/man/celdaClusters.Rd +++ b/man/celdaClusters.Rd @@ -26,13 +26,13 @@ celdaClusters(x, altExpName = "featureSubset") <- value \item A \linkS4class{SingleCellExperiment} object returned by \link{celda_C}, or \link{celda_CG}, with the matrix located in the \code{useAssay} assay slot. The -a \link[SingleCellExperiment]{altExp} slot with name \code{altExpName} will +a \link{altExp} slot with name \code{altExpName} will be used. Rows represent features and columns represent cells. \item Celda model object.}} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{value}{Character vector of cell cluster labels for replacements. Works diff --git a/man/celdaGridSearch.Rd b/man/celdaGridSearch.Rd index a5a0c1b3..144f2fae 100644 --- a/man/celdaGridSearch.Rd +++ b/man/celdaGridSearch.Rd @@ -51,9 +51,9 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{model}{Celda model. Options available in \link{availableModels}.} @@ -98,7 +98,7 @@ and main process. Default "Celda".} \value{ A \linkS4class{SingleCellExperiment} object. Function parameter settings and celda model results are stored in the - \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. + \link{metadata} \code{"celda_grid_search"} slot. } \description{ Run Celda with different combinations of parameters and diff --git a/man/celdaHeatmap.Rd b/man/celdaHeatmap.Rd index 80c87f60..b1ef07fc 100644 --- a/man/celdaHeatmap.Rd +++ b/man/celdaHeatmap.Rd @@ -22,10 +22,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} \item{...}{Additional parameters passed to \link{plotHeatmap}.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{featureIx}{Integer vector. Select features for display in heatmap. If diff --git a/man/celdaModel.Rd b/man/celdaModel.Rd index 0f3dafb3..0bbdb789 100644 --- a/man/celdaModel.Rd +++ b/man/celdaModel.Rd @@ -16,7 +16,7 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/celdaModules.Rd b/man/celdaModules.Rd index 1bb45f90..d73cbf28 100644 --- a/man/celdaModules.Rd +++ b/man/celdaModules.Rd @@ -22,7 +22,7 @@ celdaModules(sce, altExpName = "featureSubset") <- value located in the \code{useAssay} assay slot. Rows represent features and columns represent cells.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{value}{Character vector of feature module labels for replacements. diff --git a/man/celdaProbabilityMap.Rd b/man/celdaProbabilityMap.Rd index 1a30226d..aad40557 100644 --- a/man/celdaProbabilityMap.Rd +++ b/man/celdaProbabilityMap.Rd @@ -32,10 +32,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} \item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{level}{Character. One of "cellPopulation" or "Sample". diff --git a/man/celdaTsne.Rd b/man/celdaTsne.Rd index 7dc6d3c2..dbeacc65 100644 --- a/man/celdaTsne.Rd +++ b/man/celdaTsne.Rd @@ -30,10 +30,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \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 \value{ \code{sce} with t-SNE coordinates (columns "celda_tSNE1" & "celda_tSNE2") added to - \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_tSNE")}. + \code{\link{reducedDim}(sce, "celda_tSNE")}. } \description{ Embeds cells in two dimensions using \link[Rtsne]{Rtsne} based diff --git a/man/celdaUmap.Rd b/man/celdaUmap.Rd index d28ecf5f..18e37401 100644 --- a/man/celdaUmap.Rd +++ b/man/celdaUmap.Rd @@ -34,10 +34,10 @@ returned by \link{celda_C}, \link{celda_G}, or \link{celda_CG}.} \item{...}{Additional parameters to pass to \link[uwot]{umap}.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \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 \value{ \code{sce} with UMAP coordinates (columns "celda_UMAP1" & "celda_UMAP2") added to - \code{\link[SingleCellExperiment]{reducedDim}(sce, "celda_UMAP")}. + \code{\link{reducedDim}(sce, "celda_UMAP")}. } \description{ Embeds cells in two dimensions using \link[uwot]{umap} based on diff --git a/man/celda_C.Rd b/man/celda_C.Rd index ba7bb707..f3a25855 100644 --- a/man/celda_C.Rd +++ b/man/celda_C.Rd @@ -62,9 +62,9 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \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.} } \value{ A \link[SingleCellExperiment]{SingleCellExperiment} object. Function - parameter settings are stored in the \link[S4Vectors]{metadata} + parameter settings are stored in the \link{metadata} \code{"celda_parameters"} slot. Columns \code{celda_sample_label} and \code{celda_cell_cluster} in - \link[SummarizedExperiment]{colData} contain sample labels and celda cell + \link{colData} contain sample labels and celda cell population clusters. } \description{ Clusters the columns of a count matrix containing single-cell data into K subpopulations. The - \code{useAssay} \link[SummarizedExperiment]{assay} slot in - \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if + \code{useAssay} \link{assay} slot in + \code{altExpName} \link{altExp} slot will be used if it exists. Otherwise, the \code{useAssay} - \link[SummarizedExperiment]{assay} slot in \code{x} will be used if + \link{assay} slot in \code{x} will be used if \code{x} is a \linkS4class{SingleCellExperiment} object. } \examples{ diff --git a/man/celda_CG.Rd b/man/celda_CG.Rd index f8b843df..3d5d7555 100644 --- a/man/celda_CG.Rd +++ b/man/celda_CG.Rd @@ -65,16 +65,16 @@ celda_CG(x, ...) \arguments{ \item{x}{A numeric \link{matrix} of counts or a \linkS4class{SingleCellExperiment} -with the matrix located in the \link[SummarizedExperiment]{assay} +with the matrix located in the \link{assay} slot under \code{useAssay} in \code{altExp(x, altExpName)}. Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{sampleLabel}{Vector or factor. Denotes the sample label for each cell @@ -107,12 +107,13 @@ likelihood to stop inference. Default 10.} \item{maxIter}{Integer. Maximum number of iterations of Gibbs sampling to perform. Default 200.} -\item{splitOnIter}{Integer. On every `splitOnIter` iteration, a heuristic +\item{splitOnIter}{Integer. On every \code{splitOnIter} iteration, +a heuristic will be applied to determine if a cell population or feature module should be reassigned and another cell population or feature module should be split into two clusters. To disable splitting, set to -1. Default 10.} -\item{splitOnLast}{Integer. After `stopIter` iterations have been +\item{splitOnLast}{Integer. After \code{stopIter} iterations have been performed without improvement, a heuristic will be applied to determine if a cell population or feature module should be reassigned and another cell 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 With 'random', cells are randomly assigned to a populations. With 'split', cells will be split into sqrt(K) populations and then each popluation will be subsequently split into another sqrt(K) populations. With 'predefined', -values in `zInit` will be used to initialize `z`. Default 'split'.} +values in \code{zInit} will be used to initialize \code{z}. Default 'split'.} \item{yInitialize}{Chararacter. One of 'random', 'split', or 'predefined'. With 'random', features are randomly assigned to a modules. With 'split', features will be split into sqrt(L) modules and then each module will be subsequently split into another sqrt(L) modules. With 'predefined', values -in `yInit` will be used to initialize `y`. Default 'split'.} +in \code{yInit} will be used to initialize \code{y}. Default 'split'.} -\item{countChecksum}{Character. An MD5 checksum for the `counts` matrix. +\item{countChecksum}{Character. An MD5 checksum for the counts matrix. Default NULL.} \item{zInit}{Integer vector. Sets initial starting values of z. If NULL, starting values for each cell will be randomly sampled from 1:K. 'zInit' -can only be used when `initialize' = 'random'`. Default NULL.} +can only be used when \code{initialize = "random"}. Default NULL.} \item{yInit}{Integer vector. Sets initial starting values of y. If NULL, starting values for each feature will be randomly sampled from 1:L. -'yInit' can only be used when `initialize = 'random'`. Default NULL.} +'yInit' can only be used when \code{initialize = "random"}. Default NULL.} \item{logfile}{Character. Messages will be redirected to a file named `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. } \value{ A \linkS4class{SingleCellExperiment} object. Function - parameter settings are stored in \link[S4Vectors]{metadata} - \code{"celda_parameters"} in \link[SingleCellExperiment]{altExp} slot. - In \link[SingleCellExperiment]{altExp} slot, + parameter settings are stored in \link{metadata} + \code{"celda_parameters"} in \link{altExp} slot. + In \link{altExp} slot, columns \code{celda_sample_label} and \code{celda_cell_cluster} in - \link[SummarizedExperiment]{colData} contain sample labels and celda cell + \link{colData} contain sample labels and celda cell population clusters. Column \code{celda_feature_module} in - \link[SummarizedExperiment]{rowData} contains feature modules. + \link{rowData} contains feature modules. } \description{ Clusters the rows and columns of a count matrix containing single-cell data into L modules and K subpopulations, respectively. The - \code{useAssay} \link[SummarizedExperiment]{assay} slot in - \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if + \code{useAssay} \link{assay} slot in + \code{altExpName} \link{altExp} slot will be used if it exists. Otherwise, the \code{useAssay} - \link[SummarizedExperiment]{assay} slot in \code{x} will be used if + \link{assay} slot in \code{x} will be used if \code{x} is a \linkS4class{SingleCellExperiment} object. } \examples{ diff --git a/man/celda_G.Rd b/man/celda_G.Rd index 86f3892f..f8d98b40 100644 --- a/man/celda_G.Rd +++ b/man/celda_G.Rd @@ -59,9 +59,9 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{L}{Integer. Number of feature modules.} @@ -118,17 +118,17 @@ starting values for each feature will be randomly sampled from `1:L`. } \value{ A \linkS4class{SingleCellExperiment} object. Function - parameter settings are stored in the \link[S4Vectors]{metadata} + parameter settings are stored in the \link{metadata} \code{"celda_parameters"} slot. Column \code{celda_feature_module} in - \link[SummarizedExperiment]{rowData} contains feature modules. + \link{rowData} contains feature modules. } \description{ Clusters the rows of a count matrix containing single-cell data into L modules. The - \code{useAssay} \link[SummarizedExperiment]{assay} slot in - \code{altExpName} \link[SingleCellExperiment]{altExp} slot will be used if + \code{useAssay} \link{assay} slot in + \code{altExpName} \link{altExp} slot will be used if it exists. Otherwise, the \code{useAssay} - \link[SummarizedExperiment]{assay} slot in \code{x} will be used if + \link{assay} slot in \code{x} will be used if \code{x} is a \linkS4class{SingleCellExperiment} object. } \examples{ diff --git a/man/celdatosce.Rd b/man/celdatosce.Rd index b577cbd3..aca4227a 100644 --- a/man/celdatosce.Rd +++ b/man/celdatosce.Rd @@ -49,19 +49,19 @@ using older versions of \code{celda}.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ A \linkS4class{SingleCellExperiment} object. Function - parameter settings are stored in the \link[S4Vectors]{metadata} + parameter settings are stored in the \link{metadata} \code{"celda_parameters"} slot. Columns \code{celda_sample_label} and \code{celda_cell_cluster} in - \link[SummarizedExperiment]{colData} contain sample labels and celda cell + \link{colData} contain sample labels and celda cell population clusters. Column \code{celda_feature_module} in - \link[SummarizedExperiment]{rowData} contain feature modules. + \link{rowData} contain feature modules. } \description{ Convert a old celda model object (\code{celda_C}, diff --git a/man/clusterProbability.Rd b/man/clusterProbability.Rd index f01bb94b..295cffea 100644 --- a/man/clusterProbability.Rd +++ b/man/clusterProbability.Rd @@ -23,10 +23,10 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{log}{Logical. If \code{FALSE}, then the normalized conditional diff --git a/man/differentialExpression.Rd b/man/differentialExpression.Rd index 20501c23..7a623670 100644 --- a/man/differentialExpression.Rd +++ b/man/differentialExpression.Rd @@ -39,11 +39,11 @@ labels in \code{celdaClusters(x, altExpName = altExpName)} if \code{x} is a \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{c1}{Integer vector. Cell populations to include in group 1 for the diff --git a/man/factorizeMatrix.Rd b/man/factorizeMatrix.Rd index dbb900bf..648d6368 100644 --- a/man/factorizeMatrix.Rd +++ b/man/factorizeMatrix.Rd @@ -40,11 +40,11 @@ counts matrix.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{type}{Character vector. A vector containing one or more of "counts", diff --git a/man/featureModuleLookup.Rd b/man/featureModuleLookup.Rd index dbd980a8..16a33377 100644 --- a/man/featureModuleLookup.Rd +++ b/man/featureModuleLookup.Rd @@ -25,7 +25,7 @@ Rows represent features and columns represent cells.} \item{feature}{Character vector. Identify feature modules for the specified feature names. \code{feature} must match the rownames of \code{sce}.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{exactMatch}{Logical. Whether to look for exactMatch of the gene name diff --git a/man/featureModuleTable.Rd b/man/featureModuleTable.Rd index 9d7eb4b1..9be698e5 100644 --- a/man/featureModuleTable.Rd +++ b/man/featureModuleTable.Rd @@ -17,10 +17,10 @@ featureModuleTable( located in the \code{useAssay} assay slot. Rows represent features and columns represent cells.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{outputFile}{File name for feature module table. If NULL, file will diff --git a/man/findMarkersTree.Rd b/man/findMarkersTree.Rd index ff7d0585..503eeadb 100644 --- a/man/findMarkersTree.Rd +++ b/man/findMarkersTree.Rd @@ -51,11 +51,11 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{class}{Vector of cell cluster labels.} diff --git a/man/geneSetEnrich.Rd b/man/geneSetEnrich.Rd index 4dc8b492..04e2b43d 100644 --- a/man/geneSetEnrich.Rd +++ b/man/geneSetEnrich.Rd @@ -27,11 +27,11 @@ matrix or \linkS4class{SingleCellExperiment} object should be gene names.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{databases}{Character vector. Name of reference database. Available diff --git a/man/logLikelihood.Rd b/man/logLikelihood.Rd index 4e992c2a..f0f647e2 100644 --- a/man/logLikelihood.Rd +++ b/man/logLikelihood.Rd @@ -29,10 +29,10 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/logLikelihoodHistory.Rd b/man/logLikelihoodHistory.Rd index 4fc161cb..58638a94 100644 --- a/man/logLikelihoodHistory.Rd +++ b/man/logLikelihoodHistory.Rd @@ -19,7 +19,7 @@ model object.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/moduleHeatmap.Rd b/man/moduleHeatmap.Rd index e3e42fe4..9b235af4 100644 --- a/man/moduleHeatmap.Rd +++ b/man/moduleHeatmap.Rd @@ -46,11 +46,11 @@ Rows represent features and columns represent cells.} \item{...}{Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{featureModule}{Integer Vector. The featureModule(s) to display. diff --git a/man/perplexity.Rd b/man/perplexity.Rd index 78c6363f..6f12caea 100644 --- a/man/perplexity.Rd +++ b/man/perplexity.Rd @@ -39,11 +39,11 @@ counts matrix.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{newCounts}{A new counts matrix used to calculate perplexity. If NULL, diff --git a/man/plotCeldaViolin.Rd b/man/plotCeldaViolin.Rd index f1f7843c..6806929c 100644 --- a/man/plotCeldaViolin.Rd +++ b/man/plotCeldaViolin.Rd @@ -36,11 +36,11 @@ represent features and columns represent cells.} \item{features}{Character vector. Uses these genes for plotting.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{exactMatch}{Logical. Whether an exact match or a partial match using diff --git a/man/plotDimReduceCluster.Rd b/man/plotDimReduceCluster.Rd index 2124a739..cdafb9cf 100644 --- a/man/plotDimReduceCluster.Rd +++ b/man/plotDimReduceCluster.Rd @@ -49,7 +49,7 @@ column in \code{colData(x)}.} \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and \code{dim2} are set.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{dim1}{Numeric vector. First dimension from data diff --git a/man/plotDimReduceFeature.Rd b/man/plotDimReduceFeature.Rd index 1e8719a3..22378e72 100644 --- a/man/plotDimReduceFeature.Rd +++ b/man/plotDimReduceFeature.Rd @@ -73,11 +73,11 @@ dimension reduction output.} \item{dim2}{Numeric vector. Second dimension from data dimension reduction output.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{features}{Character vector. Features in the rownames of counts to plot.} @@ -99,7 +99,7 @@ and standard deviation of 1. Default \code{TRUE}.} and upper bounds for the data. This threshold is applied after row scaling. Set to NULL to disable. Default \code{c(-1,1)}.} -\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range +\item{limits}{Passed to \link{scale_colour_gradient2}. The range of color scale.} \item{size}{Numeric. Sets size of point on plot. Default 1.} diff --git a/man/plotDimReduceGrid.Rd b/man/plotDimReduceGrid.Rd index 138b4fc6..6b9ad749 100644 --- a/man/plotDimReduceGrid.Rd +++ b/man/plotDimReduceGrid.Rd @@ -65,11 +65,11 @@ reduction output.} \item{dim2}{Numeric vector. Second dimension from data dimension reduction output.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{size}{Numeric. Sets size of point on plot. Default 1.} @@ -78,7 +78,7 @@ to use. Default "featureSubset".} \item{ylab}{Character vector. Label for the y-axis. Default 'Dimension_2'.} -\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient2}. The range +\item{limits}{Passed to \link{scale_colour_gradient2}. The range of color scale.} \item{colorLow}{Character. A color available from `colors()`. diff --git a/man/plotDimReduceModule.Rd b/man/plotDimReduceModule.Rd index d3b717f5..be8fbcc0 100644 --- a/man/plotDimReduceModule.Rd +++ b/man/plotDimReduceModule.Rd @@ -63,11 +63,11 @@ First dimension from data dimension reduction output.} \item{dim2}{Numeric vector. Second dimension from data dimension reduction output.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{modules}{Character vector. Module(s) from celda model to be plotted. @@ -76,7 +76,7 @@ e.g. c("1", "2").} \item{rescale}{Logical. Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.} -\item{limits}{Passed to \link[ggplot2]{scale_colour_gradient}. The range +\item{limits}{Passed to \link{scale_colour_gradient}. The range of color scale.} \item{size}{Numeric. Sets size of point on plot. Default 1.} diff --git a/man/plotGridSearchPerplexity.Rd b/man/plotGridSearchPerplexity.Rd index aaeaaaa7..e80cd930 100644 --- a/man/plotGridSearchPerplexity.Rd +++ b/man/plotGridSearchPerplexity.Rd @@ -23,7 +23,7 @@ plotGridSearchPerplexity(x, ...) \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{sep}{Numeric. Breaks in the x axis of the resulting plot.} diff --git a/man/plotGridSearchPerplexityDiff.Rd b/man/plotGridSearchPerplexityDiff.Rd index 18497649..5b0173ea 100644 --- a/man/plotGridSearchPerplexityDiff.Rd +++ b/man/plotGridSearchPerplexityDiff.Rd @@ -23,7 +23,7 @@ plotGridSearchPerplexityDiff(x, ...) \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{sep}{Numeric. Breaks in the x axis of the resulting plot.} diff --git a/man/recodeClusterY.Rd b/man/recodeClusterY.Rd index 1fc7fceb..18d7847b 100644 --- a/man/recodeClusterY.Rd +++ b/man/recodeClusterY.Rd @@ -10,7 +10,7 @@ recodeClusterY(sce, from, to, altExpName = "featureSubset") \item{sce}{\linkS4class{SingleCellExperiment} object returned from \link{celda_G} or \link{celda_CG}. Must contain column \code{celda_feature_module} in -\code{\link[SummarizedExperiment]{rowData}(altExp(sce, altExpName))}.} +\code{\link{rowData}(altExp(sce, altExpName))}.} \item{from}{Numeric vector. Unique values in the range of \code{seq(celdaModules(sce))} that correspond to the original module labels @@ -19,7 +19,7 @@ in \code{sce}.} \item{to}{Numeric vector. Unique values in the range of \code{seq(celdaModules(sce))} that correspond to the new module labels.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/recodeClusterZ.Rd b/man/recodeClusterZ.Rd index e1a11e50..eb9032ee 100644 --- a/man/recodeClusterZ.Rd +++ b/man/recodeClusterZ.Rd @@ -10,7 +10,7 @@ recodeClusterZ(sce, from, to, altExpName = "featureSubset") \item{sce}{\linkS4class{SingleCellExperiment} object returned from \link{celda_C} or \link{celda_CG}. Must contain column \code{celda_cell_cluster} in -\code{\link[SummarizedExperiment]{colData}(altExp(sce, altExpName))}.} +\code{\link{colData}(altExp(sce, altExpName))}.} \item{from}{Numeric vector. Unique values in the range of \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to @@ -21,7 +21,7 @@ labels in \code{sce}.} \code{seq(celdaClusters(sce, altExpName = altExpName))} that correspond to the new cluster labels.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/recursiveSplitCell.Rd b/man/recursiveSplitCell.Rd index f9a9a93c..09e48ff3 100644 --- a/man/recursiveSplitCell.Rd +++ b/man/recursiveSplitCell.Rd @@ -59,10 +59,10 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{sampleLabel}{Vector or factor. Denotes the sample label for each cell @@ -123,7 +123,7 @@ If FALSE, then perplexity can be calculated later with \value{ A \linkS4class{SingleCellExperiment} object. Function parameter settings and celda model results are stored in the - \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in + \link{metadata} \code{"celda_grid_search"} slot. The models in the list will be of class \code{celda_C} if \code{yInit = NULL} or \code{celda_CG} if \code{zInit} is set. } diff --git a/man/recursiveSplitModule.Rd b/man/recursiveSplitModule.Rd index 822cc845..56e2021e 100644 --- a/man/recursiveSplitModule.Rd +++ b/man/recursiveSplitModule.Rd @@ -58,11 +58,11 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \link[SingleCellExperiment]{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{initialL}{Integer. Minimum number of modules to try.} @@ -121,7 +121,7 @@ If FALSE, then perplexity can be calculated later with \value{ A \linkS4class{SingleCellExperiment} object. Function parameter settings and celda model results are stored in the - \link[S4Vectors]{metadata} \code{"celda_grid_search"} slot. The models in + \link{metadata} \code{"celda_grid_search"} slot. The models in the list will be of class \link{celda_G} if \code{zInit = NULL} or \link{celda_CG} if \code{zInit} is set. } diff --git a/man/resList.Rd b/man/resList.Rd index 316b7f4a..4bf32a76 100644 --- a/man/resList.Rd +++ b/man/resList.Rd @@ -19,7 +19,7 @@ resList(x, ...) \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/resamplePerplexity.Rd b/man/resamplePerplexity.Rd index 512bbe50..701dbc8c 100644 --- a/man/resamplePerplexity.Rd +++ b/man/resamplePerplexity.Rd @@ -29,11 +29,11 @@ Rows represent features and columns represent cells. Must contain \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use if \code{x} is a \linkS4class{SingleCellExperiment} object. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{resample}{Integer. The number of times to resample the counts matrix diff --git a/man/runParams.Rd b/man/runParams.Rd index 86018aaa..0bbab931 100644 --- a/man/runParams.Rd +++ b/man/runParams.Rd @@ -19,7 +19,7 @@ runParams(x, ...) \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ diff --git a/man/sampleLabel.Rd b/man/sampleLabel.Rd index 3dcb99a4..ea7b450e 100644 --- a/man/sampleLabel.Rd +++ b/man/sampleLabel.Rd @@ -30,7 +30,7 @@ Rows represent features and columns represent cells. \item{...}{Ignored. Placeholder to prevent check warning.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{value}{Character vector of sample labels for replacements. Works diff --git a/man/selectBestModel.Rd b/man/selectBestModel.Rd index 19fb92a9..811aaa52 100644 --- a/man/selectBestModel.Rd +++ b/man/selectBestModel.Rd @@ -28,7 +28,7 @@ best model as a \code{celdaList} object or not. If \code{FALSE}, return the best model as a corresponding celda model object.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ @@ -39,10 +39,10 @@ One of \code{metadata(x)}. If there is only one set of parameters, a new \linkS4class{SingleCellExperiment} object with the matching model stored in the - \link[S4Vectors]{metadata} + \link{metadata} \code{"celda_parameters"} slot will be returned. Otherwise, a new \linkS4class{SingleCellExperiment} object with the subset models stored - in the \link[S4Vectors]{metadata} + in the \link{metadata} \code{"celda_grid_search"} slot will be returned. \item A new \code{celdaList} object containing one model with the best log-likelihood for each set of parameters. If only one set of parameters diff --git a/man/selectFeatures.Rd b/man/selectFeatures.Rd index f1b47207..75d706e9 100644 --- a/man/selectFeatures.Rd +++ b/man/selectFeatures.Rd @@ -37,15 +37,15 @@ Rows represent features and columns represent cells.} \item{minCell}{Minimum number of cells required for feature selection.} \item{useAssay}{A string specifying the name of the -\link[SummarizedExperiment]{assay} slot to use. Default "counts".} +\link{assay} slot to use. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ A \linkS4class{SingleCellExperiment} object with a - \code{altExpName} \link[SingleCellExperiment]{altExp} slot. Function - parameter settings are stored in the \link[S4Vectors]{metadata} + \code{altExpName} \link{altExp} slot. Function + parameter settings are stored in the \link{metadata} \code{"select_features"} slot. } \description{ @@ -53,8 +53,8 @@ A simple heuristic feature selection procedure. Select features with at least \code{minCount} counts in at least \code{minCell} cells. A \linkS4class{SingleCellExperiment} object with subset features will be stored in the - \link[SingleCellExperiment]{altExp} slot with name \code{altExpName}. - The name of the \code{assay} slot in \link[SingleCellExperiment]{altExp} + \link{altExp} slot with name \code{altExpName}. + The name of the \code{assay} slot in \link{altExp} will be the same as \code{useAssay}. } \examples{ diff --git a/man/simulateCells.Rd b/man/simulateCells.Rd index 67451338..8c63feec 100644 --- a/man/simulateCells.Rd +++ b/man/simulateCells.Rd @@ -70,13 +70,13 @@ a default value of 12345 is used. If NULL, no calls to \value{ A \link[SingleCellExperiment]{SingleCellExperiment} object with simulated count matrix stored in the "counts" assay slot. Function - parameter settings are stored in the \link[S4Vectors]{metadata} slot. For + parameter settings are stored in the \link{metadata} slot. For \code{"celda_CG"} and \code{"celda_C"} models, columns \code{celda_sample_label} and \code{celda_cell_cluster} in - \link[SummarizedExperiment]{colData} contain simulated sample labels and + \link{colData} contain simulated sample labels and cell population clusters. For \code{"celda_CG"} and \code{"celda_G"} models, column \code{celda_feature_module} in - \link[SummarizedExperiment]{rowData} contains simulated gene modules. + \link{rowData} contains simulated gene modules. } \description{ This function generates a \linkS4class{SingleCellExperiment} diff --git a/man/splitModule.Rd b/man/splitModule.Rd index 4c2a19a5..a962e2cc 100644 --- a/man/splitModule.Rd +++ b/man/splitModule.Rd @@ -23,10 +23,10 @@ Rows represent features and columns represent cells.} \item{...}{Ignored. Placeholder to prevent check warning.} -\item{useAssay}{A string specifying which \link[SummarizedExperiment]{assay} +\item{useAssay}{A string specifying which \link{assay} slot to use for \code{x}. Default "counts".} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} \item{module}{Integer. The module to be split.} @@ -41,7 +41,7 @@ a default value of 12345 is used. If NULL, no calls to \value{ A updated \linkS4class{SingleCellExperiment} object with new feature modules stored in column \code{celda_feature_module} in - \code{\link[SummarizedExperiment]{rowData}(x)}. + \code{\link{rowData}(x)}. } \description{ Manually select a celda feature module to split into 2 or diff --git a/man/subsetCeldaList.Rd b/man/subsetCeldaList.Rd index 0aee44f4..7a40db78 100644 --- a/man/subsetCeldaList.Rd +++ b/man/subsetCeldaList.Rd @@ -27,7 +27,7 @@ subsetCeldaList(x, ...) \item{params}{List. List of parameters used to subset the matching celda models in list \code{"celda_grid_search"} in \code{metadata(x)}.} -\item{altExpName}{The name for the \link[SingleCellExperiment]{altExp} slot +\item{altExpName}{The name for the \link{altExp} slot to use. Default "featureSubset".} } \value{ @@ -39,10 +39,10 @@ One of \code{"celda_grid_search"} slot in \code{metadata(x)} matches the given criteria, a new \linkS4class{SingleCellExperiment} object with the matching model stored in the - \link[S4Vectors]{metadata} + \link{metadata} \code{"celda_parameters"} slot will be returned. Otherwise, a new \linkS4class{SingleCellExperiment} object with the subset models stored - in the \link[S4Vectors]{metadata} + in the \link{metadata} \code{"celda_grid_search"} slot will be returned. \item A new \code{celdaList} object containing all models matching the provided criteria in \code{params}. If only one item in the