Merge pull request #69 from Artur-man/main

update documentation and fix doc bugs
BIMSBbioinfo · Dec 15, 2023 · 9a05b6f · 9a05b6f
2 parents 8f367d5 + d81195e
commit 9a05b6f
Show file tree

Hide file tree

Showing 32 changed files with 1 addition and 183 deletions.
diff --git a/R/generics.R b/R/generics.R
@@ -9,8 +9,6 @@ NULL
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return Returns object after normalization
-#'
 #' @rdname normalizeData
 #' @export
 #'
@@ -25,8 +23,6 @@ normalizeData <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{Metadata}: The name of the default assay
-#'
 #' @rdname Metadata
 #' @export Metadata
 #'
@@ -38,8 +34,6 @@ Metadata <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value metadata
 #'
-#' @return \code{Metadata<-}: The coordinates updated
-#'
 #' @rdname Metadata
 #' @export Metadata<-
 #'
@@ -54,8 +48,6 @@ Metadata <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{SampleMetadata}: The name of the default assay
-#'
 #' @rdname SampleMetadata
 #' @export SampleMetadata
 #'
@@ -70,8 +62,6 @@ SampleMetadata <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{addAssay}: The name of the default assay
-#'
 #' @rdname addAssay
 #' @export addAssay
 #'
@@ -86,8 +76,6 @@ addAssay <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrAssayNames}: The name of the default assay
-#'
 #' @rdname vrAssayNames
 #' @export vrAssayNames
 #'
@@ -99,8 +87,6 @@ vrAssayNames <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value assay name
 #'
-#' @return \code{vrAssayNames<-}: The coordinates updated
-#'
 #' @rdname vrAssayNames
 #' @export vrAssayNames<-
 #'
@@ -115,8 +101,6 @@ vrAssayNames <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrEmbeddingNames}: The name of embeddings
-#'
 #' @rdname vrEmbeddingNames
 #' @export vrEmbeddingNames
 #'
@@ -131,8 +115,6 @@ vrEmbeddingNames <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{changeSampleNames}: The name of the default assay
-#'
 #' @rdname changeSampleNames
 #' @export changeSampleNames
 #'
@@ -148,8 +130,6 @@ changeSampleNames <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrAssayTypes}: The name of the default assay
-#'
 #' @rdname vrAssayTypes
 #' @export vrAssayTypes
 #'
@@ -164,8 +144,6 @@ vrAssayTypes <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrMainAssay}: The name of the default assay
-#'
 #' @rdname vrMainAssay
 #' @export vrMainAssay
 #'
@@ -177,8 +155,6 @@ vrMainAssay <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value assay name
 #'
-#' @return \code{vrMainAssay<-}: The name of the default assay updated
-#'
 #' @rdname vrMainAssay
 #' @export vrMainAssay<-
 #'
@@ -232,8 +208,6 @@ vrFeatures <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrFeatureData}: The name of the default assay
-#'
 #' @rdname vrFeatureData
 #' @export vrFeatureData
 #'
@@ -259,8 +233,6 @@ vrFeatureData <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrData}: The name of the default assay
-#'
 #' @rdname vrData
 #' @export vrData
 #'
@@ -275,8 +247,6 @@ vrData <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrGraph}: The name of the default assay
-#'
 #' @rdname vrGraph
 #' @export vrGraph
 #'
@@ -288,8 +258,6 @@ vrGraph <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value an igraph object
 #'
-#' @return \code{vrGraph<-}: graph updated
-#'
 #' @rdname vrGraph
 #' @export vrGraph<-
 #'
@@ -304,8 +272,6 @@ vrGraph <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrGraphNames}: The names of all graphs
-#'
 #' @rdname vrGraphNames
 #' @export vrGraphNames
 #'
@@ -321,8 +287,6 @@ vrGraphNames <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return Returns object after normalization
-#'
 #' @rdname getProfileNeighbors
 #' @export getProfileNeighbors
 #'
@@ -337,8 +301,6 @@ getProfileNeighbors <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return Returns object after normalization
-#'
 #' @rdname getSpatialNeighbors
 #' @export getSpatialNeighbors
 #'
@@ -353,8 +315,6 @@ getSpatialNeighbors <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return Returns object after normalization
-#'
 #' @rdname getFeatures
 #' @export getFeatures
 #'
@@ -370,8 +330,6 @@ getFeatures <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrCoordinates}: The name of the default assay
-#'
 #' @rdname vrCoordinates
 #' @export vrCoordinates
 #'
@@ -383,8 +341,6 @@ vrCoordinates <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value coordinates
 #'
-#' @return \code{vrCoordinates<-}: The coordinates updated
-#'
 #' @rdname vrCoordinates
 #' @export vrCoordinates<-
 #'
@@ -399,8 +355,6 @@ vrCoordinates <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{flipCoordinates}: The name of the default assay
-#'
 #' @rdname flipCoordinates
 #' @export flipCoordinates
 #'
@@ -415,8 +369,6 @@ flipCoordinates <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrSegments}: The name of the default assay
-#'
 #' @rdname vrSegments
 #' @export vrSegments
 #'
@@ -428,8 +380,6 @@ vrSegments <- function(object, ...) {
 #' @param ... Arguments passed to other methods
 #' @param value segments
 #'
-#' @return \code{vrSegments<-}: The coordinates updated
-#'
 #' @rdname vrSegments
 #' @export vrSegments<-
 #'
@@ -444,8 +394,6 @@ vrSegments <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrDistances}: The name of the default assay
-#'
 #' @rdname vrDistances
 #' @export vrDistances
 #'
@@ -460,8 +408,6 @@ vrDistances <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrEmbeddings}: The name of the default assay
-#'
 #' @rdname vrEmbeddings
 #' @export vrEmbeddings
 #'
@@ -515,8 +461,6 @@ getUMAP <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrImages}: The name of the default assay
-#'
 #' @rdname vrImages
 #' @export vrImages
 #'
@@ -542,8 +486,6 @@ vrImages <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrImageNames}: The name of the default assay
-#'
 #' @rdname vrImageNames
 #' @export vrImageNames
 #'
@@ -558,8 +500,6 @@ vrImageNames <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrMainImage}: The name of the default assay
-#'
 #' @rdname vrMainImage
 #' @export vrMainImage
 #'
@@ -574,12 +514,10 @@ vrMainImage <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{vrMainImage}: The name of the default assay
-#'
 #' @rdname vrMainImage
 #' @export vrMainImage<-
 #'
-"vrMainImage<-" <- function(object, ...) {
+"vrMainImage<-" <- function(object, ..., value) {
   UseMethod(generic = 'vrMainImage<-', object = object)
 }
 
@@ -591,8 +529,6 @@ vrMainImage <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{resizeImage}: The name of the default assay
-#'
 #' @rdname resizeImage
 #' @export resizeImage
 #'
@@ -607,7 +543,6 @@ resizeImage <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{modulateImage}: The name of the default assay
 #'
 #' @rdname modulateImage
 #' @export modulateImage
@@ -623,8 +558,6 @@ modulateImage <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{as.Seurat}: The name of the default assay
-#'
 #' @rdname as.Seurat
 #' @export as.Seurat
 #'
@@ -639,8 +572,6 @@ as.Seurat <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{as.AnnData}: The name of the default assay
-#'
 #' @rdname as.AnnData
 #' @export as.AnnData
 #'
@@ -657,8 +588,6 @@ as.AnnData <- function(object, ...) {
 #' @param image_id image name
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{as.Zarr}: The name of the default assay
-#'
 #' @rdname as.Zarr
 #' @export as.Zarr
 #'
@@ -674,8 +603,6 @@ as.Zarr <- function(object, out_path, image_id, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{as.Giotto}: The name of the default assay
-#'
 #' @rdname as.Giotto
 #' @export as.Giotto
 #'
@@ -690,8 +617,6 @@ as.Giotto <- function(object, ...) {
 #' @param object An object
 #' @param ... Arguments passed to other methods
 #'
-#' @return \code{as.VoltRon}: The name of the default assay
-#'
 #' @rdname as.VoltRon
 #' @export as.VoltRon
 #'

diff --git a/man/AddAssay.Rd b/man/AddAssay.Rd
diff --git a/man/Metadata.Rd b/man/Metadata.Rd
diff --git a/man/NormalizeData.Rd b/man/NormalizeData.Rd
diff --git a/man/SampleMetadata.Rd b/man/SampleMetadata.Rd
diff --git a/man/as.AnnData.Rd b/man/as.AnnData.Rd