Update docs

R/generics.R

@@ -19,7 +19,7 @@ NULL
 #'
 #' @aliases SeuratAccess
 #'
-#' @concept unsorted
+#' @concept seurat
 #'
 #' @examples
 #' cluster_letters <- LETTERS[Idents(object = pbmc_small)]
@@ -82,7 +82,7 @@ as.Neighbor <- function(x, ...) {
 #' @rdname as.Seurat
 #' @export as.Seurat
 #'
-#' @concept conversion
+#' @concept seurat
 #'
 as.Seurat <- function(x, ...) {
   UseMethod(generic = 'as.Seurat', object = x)
@@ -221,6 +221,8 @@ DefaultAssay <- function(object, ...) {
 #' @rdname Distances
 #' @export Distances
 #'
+#' @concept data-access
+#'
 Distances <- function(object, ...) {
   UseMethod(generic = 'Distances', object = object)
 }
@@ -367,7 +369,7 @@ HVFInfo <- function(object, selection.method, status = FALSE, ...) {
 #' @rdname Idents
 #' @export Idents
 #'
-#' @concept data-access
+#' @concept seurat
 #'
 #' @examples
 #' # Get cell identity classes
@@ -410,6 +412,8 @@ Idents <- function(object, ... ) {
 #' @rdname Index
 #' @export Index
 #'
+#' @concept data-access
+#'
 Index <- function(object, ...) {
   UseMethod(generic = "Index", object = object)
 }
@@ -435,6 +439,8 @@ Index <- function(object, ...) {
 #' @rdname Indices
 #' @export Indices
 #'
+#' @concept data-access
+#'
 Indices <- function(object, ...) {
   UseMethod(generic = "Indices", object = object)
 }
@@ -598,6 +604,8 @@ Project <- function(object, ...) {
 #' @rdname Radius
 #' @export Radius
 #'
+#' @concept spatialimage
+#'
 Radius <- function(object) {
   UseMethod(generic = 'Radius', object = object)
 }
@@ -719,7 +727,7 @@ StashIdent <- function(object, save.name, ...) {
 #' @rdname Stdev
 #' @export Stdev
 #'
-#' @concept unsorted
+#' @concept data-access
 #'
 Stdev <- function(object, ...) {
   UseMethod(generic = 'Stdev', object = object)

_pkgdown.yml

@@ -34,6 +34,7 @@ reference:
   - title: The SpatialImage Class and Interaction Methods
     contents:
       - SpatialImage-class
+      - SpatialImage-methods
       - has_concept("spatialimage")
   - title: The Graph and Neighbor Classes and Interaction Methods
     contents:
@@ -53,95 +54,3 @@ reference:
       - SeuratObject-package
       - pbmc_small
       - reexports
-  - title: Unsorted
-    contents:
-      - has_concept("unsorted")
-
-# reference:
-#   - title: Main Class Definitions
-#     contents:
-#       - Seurat-class
-#       - Assay-class
-#       - DimReduc-class
-#       - Graph-class
-#       - SpatialImage-class
-#       - SeuratCommand-class
-#   - title: Other Class Definitions
-#     contents:
-#       - JackStrawData-class
-#       - has_concept("spatial-class")
-#   - title: Main Interaction Methods
-#     contents:
-#       - has_concept("seurat")
-#       - has_concept("assay")
-#       - has_concept("dimreduc")
-#       - has_concept("graph")
-#       - has_concept("spatial")
-#       - has_concept("command")
-#       - has_concept("spatial")
-#   - title: Other Interaction Methods
-#     contents:
-#       - has_concept("jackstraw")
-#       - SpatialImage-methods
-#   - title: Conversion Functions
-#     contents:
-#       - has_concept("conversion")
-#   - title: Data Loading
-#     contents:
-#       - has_concept("data-load")
-#   - title: Other Functions
-#     contents:
-#       - has_concept("data-access")
-#       - has_concept("unsorted")
-#       - has_concept("utils")
-#   - title: Internal Functions
-#     contents:
-#       - has_keyword("internal")
-#   - title: Package Information
-#     contents:
-#       - SeuratObject-package
-
-# reference:
-#   - title: Package Information
-#     contents:
-#       - SeuratObject
-#   - title: The Seurat Object
-#     contents:
-#       - Seurat-class
-#       - has_concept("seurat")
-#   - title: Assay Expression Data
-#     contents:
-#       - has_concept("assay")
-#   - title: Dimensional Reduction Information
-#     contents:
-#       - DimReduc-class
-#       - has_concept("dimreduc")
-#       - JackStrawData-class
-#       - has_concept("jackstraw")
-#   - title: Nearest Neighbor Graphs
-#     contents:
-#       - has_concept("graph")
-#   - title: Spatial Datasets
-#     contents:
-#       - SpatialImage-class
-#       - has_concept("spatial-class")
-#       - SpatialImage-methods
-#       - has_concept("spatial")
-#   - title: Command Logs
-#     contents:
-#       - has_concept("command")
-#   - title: Data Access
-#     contents:
-#       - has_concept("data-access")
-#   - title: Reading and Loading Data
-#     contents:
-#       - has_concept("data-load")
-#   - title: Conversion Utilities
-#     contents:
-#       - has_concept("conversion")
-#   - title: Unsorted
-#     contents:
-#       - has_concept("unsorted")
-#   - title: Internal
-#     contents:
-#       - has_keyword("internal")