diff --git a/R/calculate-clusters.R b/R/calculate-clusters.R index 1b50b0e..9e13fe7 100644 --- a/R/calculate-clusters.R +++ b/R/calculate-clusters.R @@ -14,13 +14,13 @@ #' have row names of cell ids (e.g., barcodes). #' @param algorithm Clustering algorithm to use. Must be one of "louvain" (default), "walktrap", or "leiden". #' @param weighting Weighting scheme to use. Must be one of "jaccard" (default), "rank", or "number" -#' @param nn Number of nearest neighbors. Default is 10. +#' @param nn Number of nearest neighbors. The default is 10. #' @param resolution Resolution parameter used by louvain and leiden clustering only. Default is 1. #' @param objective_function Leiden-specific parameter for whether to use the Constant Potts Model ("CPM"; default) or "modularity" #' @param cluster_args List of additional arguments to pass to the chosen clustering function. #' Only single values for each argument are supported (no vectors or lists). #' See igraph documentation for details on each clustering function: https://igraph.org/r/html/latest -#' @param threads Number of threads to use. Default is 1. +#' @param threads Number of threads to use. The default is 1. #' @param seed Random seed to set for clustering. #' @param pc_name Name of principal components slot in provided object. This argument is only used if a SingleCellExperiment #' or Seurat object is provided. If not provided, the SingleCellExperiment object name will default to "PCA" and the diff --git a/man/calculate_clusters.Rd b/man/calculate_clusters.Rd index 655a36c..e263dd5 100644 --- a/man/calculate_clusters.Rd +++ b/man/calculate_clusters.Rd @@ -26,7 +26,7 @@ have row names of cell ids (e.g., barcodes).} \item{weighting}{Weighting scheme to use. Must be one of "jaccard" (default), "rank", or "number"} -\item{nn}{Number of nearest neighbors. Default is 10.} +\item{nn}{Number of nearest neighbors. The default is 10.} \item{resolution}{Resolution parameter used by louvain and leiden clustering only. Default is 1.} @@ -36,7 +36,7 @@ have row names of cell ids (e.g., barcodes).} Only single values for each argument are supported (no vectors or lists). See igraph documentation for details on each clustering function: https://igraph.org/r/html/latest} -\item{threads}{Number of threads to use. Default is 1.} +\item{threads}{Number of threads to use. The default is 1.} \item{seed}{Random seed to set for clustering.}