spelling & formatting

.pre-commit-config.yaml

@@ -11,6 +11,7 @@ repos:
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: trailing-whitespace
+        exclude: 'renv/.*'
       - id: end-of-file-fixer
         exclude: '\.Rd'
 
@@ -33,43 +34,9 @@ repos:
       # codemeta must be above use-tidy-description when both are used
       # -   id: codemeta-description-updated
       - id: use-tidy-description
-      - id: spell-check
-        exclude: >
-          (?x)^(
-          .*\.[rR]|
-          .*\.feather|
-          .*\.jpeg|
-          .*\.pdf|
-          .*\.png|
-          .*\.py|
-          .*\.RData|
-          .*\.rds|
-          .*\.Rds|
-          .*\.Rproj|
-          .*\.sh|
-          (.*/|)\.gitignore|
-          (.*/|)\.gitlab-ci\.yml|
-          (.*/|)\.lintr|
-          (.*/|)\.pre-commit-.*|
-          (.*/|)\.Rbuildignore|
-          (.*/|)\.Renviron|
-          (.*/|)\.Rprofile|
-          (.*/|)\.travis\.yml|
-          (.*/|)appveyor\.yml|
-          (.*/|)DESCRIPTION|
-          (.*/|)NAMESPACE|
-          (.*/|)renv/settings\.dcf|
-          (.*/|)renv.*\.lock|
-          (.*/|)requirements.*\.in|
-          (.*/|)requirements.*\.txt|
-          (.*/|).*Dockerfile|
-          (.*/|)WORDLIST|
-          \.github/workflows/.*|
-          data/.*|
-          )$
       - id: lintr
       - id: parsable-R
       - id: no-browser-statement
       - id: no-debug-statement
       - id: deps-in-desc
-        exclude: docker/.*
+        exclude: 'docker/.*|renv/.*'

R/calculate-clusters.R

@@ -1,34 +1,37 @@
 #' Calculate graph-based clusters from a provided matrix
 #'
 #' This function is provided to simplify application of bluster package clustering functions on OpenScPCA data.
-#' In particular, this function runs bluster::clusterRows() with the bluster::NNGraphParam() function on a
+#' In particular, this function runs `bluster::clusterRows()` with the `bluster::NNGraphParam()` function on a
 #' principal components matrix, provided either directly or via single-cell object.
-#' Note that defaults for some arguments may differ from the bluster::NNGraphParam() defaults.
+#' Note that defaults for some arguments may differ from the `bluster::NNGraphParam()` defaults.
 #' Specifically, the clustering algorithm defaults to "louvain" and the weighting scheme to "jaccard"
 #' to align with common practice in scRNA-seq analysis.
 #'
 #' @import methods
 #'
 #' @param x An object containing PCs that clustering can be performed in. This can be either a SingleCellExperiment
-#'   object, a Seurat object, or a matrix where columns are PCs and rows are cells. If a matrix is provided, it must
-#'   have row names of cell ids (e.g., barcodes).
+#'   object, a Seurat object, or a matrix where columns are PCs and rows are cells.
+#'   If a matrix is provided, it must 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. 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 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
+#'   See `igraph` documentation for details on each clustering function: <https://igraph.org/r/html/latest>
 #' @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
+#' @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
 #'   Seurat object name will default to "pca".
 #'
-#' @return A data frame of cluster results with columns `cell_id` and `cluster`. Additional columns represent algorithm parameters
-#'   and include at least: `algorithm`, `weighting`, and `nn`. Louvain and leiden clustering will also include `resolution`, and
-#'   leiden clustering will further include `objective_function`.
+#' @return A data frame of cluster results with columns `cell_id` and `cluster`.
+#'   Additional columns represent algorithm parameters and include at least: `algorithm`, `weighting`, and `nn`.
+#'   Louvain and Leiden clustering will also include `resolution`,
+#'   and Leiden clustering will further include `objective_function`.
 #'
 #' @export
 #'
@@ -242,7 +245,10 @@ prepare_pc_matrix <- function(x, pc_name = NULL) {
   } else if (is(x, "SingleCellExperiment") || is(x, "Seurat")) {
     x <- extract_pc_matrix(x, pc_name = pc_name)
   } else {
-    stop("The first argument should be one of: a SingleCellExperiment object, a Seurat object, or a matrix with row names.")
+    stop(
+      "The first argument should be one of: ",
+      "a SingleCellExperiment object, a Seurat object, or a matrix with row names."
+    )
   }
 
   return(x)

rOpenScPCA.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace