Merge pull request satijalab#411 from satijalab/feat/Rproj

Utilize RStudio Projects for consistent auto-formatting of source code

.gitignore

@@ -7,4 +7,3 @@ src/*.so
 src/*.dll
 .DS_Store
 *.pdf
-*.Rproj

R/dimensional_reduction.R

@@ -1133,7 +1133,7 @@ RunUMAP.default <- function(
   reduction.key = 'UMAP_',
   assay = NULL,
   reduction.model = NULL,
-  return.model = FALSE, 
+  return.model = FALSE,
   umap.method = 'uwot',
   n.neighbors = 30L,
   n.components = 2L,
@@ -1270,7 +1270,7 @@ RunUMAP.default <- function(
           a = a,
           b = b,
           fast_sgd = uwot.sgd,
-          verbose = verbose, 
+          verbose = verbose,
           ret_model = return.model
         )
       }
@@ -1303,16 +1303,16 @@ RunUMAP.default <- function(
       if (is.list(x = object)) {
         if (packageVersion(pkg = "uwot") <= '0.1.8.9000') {
           stop("This uwot functionality requires uwot version >= 0.1.8.9000",
-               "Installing the latest version from github can be done with", 
+               "Installing the latest version from github can be done with",
                "remotes::install_github('jlmelville/uwot')")
         }
         uwot::umap_transform(
           X = NULL,
-          nn_method = object, 
-          model = model, 
+          nn_method = object,
+          model = model,
           n_threads = nbrOfWorkers(),
           n_epochs = n.epochs,
-          verbose = verbose 
+          verbose = verbose
         )
       } else {
         umap_transform(
@@ -1450,7 +1450,7 @@ RunUMAP.Graph <- function(
 #' @param assay Assay to pull data for when using \code{features}, or assay used to construct Graph
 #' if running UMAP on a Graph
 #' @param nn.name Name of knn output on which to run UMAP
-#' @param slot The slot used to pull data for when using \code{features}. data slot is by default. 
+#' @param slot The slot used to pull data for when using \code{features}. data slot is by default.
 #' @param umap.method UMAP implementation to run. Can be
 #' \describe{
 #'   \item{\code{uwot}:}{Runs umap via the uwot R package}
@@ -1521,11 +1521,11 @@ RunUMAP.Seurat <- function(
   features = NULL,
   graph = NULL,
   assay = DefaultAssay(object = object),
-  nn.name = NULL, 
+  nn.name = NULL,
   slot = 'data',
   umap.method = 'uwot',
   reduction.model = NULL,
-  return.model = FALSE, 
+  return.model = FALSE,
   n.neighbors = 30L,
   n.components = 2L,
   metric = 'cosine',

R/generics.R

@@ -72,13 +72,13 @@ as.loom <- function(x, ...) {
 }
 
 #' Convert objects to Neighbor ojbects
-#' 
+#'
 #' @param x An object to convert to \code{Neighbor}
 #' @param ... Arguments passed to other methods
-#' 
+#'
 #' @rdname as.Neighbor
 #' @export as.Neighbor
-#' 
+#'
 as.Neighbor <- function(x, ...) {
   UseMethod(generic = 'as.Neighbor', object = x)
 }
@@ -550,8 +550,8 @@ Idents <- function(object, ... ) {
   UseMethod(generic = 'Idents<-', object = object)
 }
 
-#' Get Neighbor algorithm index 
-#' 
+#' Get Neighbor algorithm index
+#'
 #' @param object An object
 #' @param ... Arguments passed to other methods;
 #'
@@ -577,7 +577,7 @@ Index <- function(object, ...) {
 }
 
 #' Get Neighbor nearest neighbor index matrices
-#' 
+#'
 #' @param object An object
 #' @param ... Arguments passed to other methods;
 #'
@@ -1180,7 +1180,7 @@ SetIdent <- function(object, ...) {
 }
 
 #' Get spatially variable feature information
-#' 
+#'
 #' @rdname SpatiallyVariableFeatures
 #' @export SpatiallyVariableFeatures
 #'