diff --git a/R/generics.R b/R/generics.R index 40c0257a..22ed2b79 100644 --- 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 index e90d847b..248cc1db 100644 --- a/man/AddAssay.Rd +++ b/man/AddAssay.Rd @@ -41,9 +41,6 @@ addAssay(object, ...) \item{layer}{layer name} } -\value{ -\code{addAssay}: The name of the default assay -} \description{ add assay to the object } diff --git a/man/Metadata.Rd b/man/Metadata.Rd index fc87671c..da7c3068 100644 --- a/man/Metadata.Rd +++ b/man/Metadata.Rd @@ -26,11 +26,6 @@ Metadata(object, ...) <- value \item{type}{the assay type: ROI, spot or cell} } -\value{ -\code{Metadata}: The name of the default assay - -\code{Metadata<-}: The coordinates updated -} \description{ Get the metadata } diff --git a/man/NormalizeData.Rd b/man/NormalizeData.Rd index ba0f14f2..90095d8a 100644 --- a/man/NormalizeData.Rd +++ b/man/NormalizeData.Rd @@ -33,9 +33,6 @@ normalizeData(object, ...) \item{sizefactor}{size factor if \code{method} is selected as \code{LogNorm}} } -\value{ -Returns object after normalization -} \description{ Normalize the count data present in a given assay. } diff --git a/man/SampleMetadata.Rd b/man/SampleMetadata.Rd index e3547d69..abe67ed3 100644 --- a/man/SampleMetadata.Rd +++ b/man/SampleMetadata.Rd @@ -14,9 +14,6 @@ SampleMetadata(object, ...) \item{...}{Arguments passed to other methods} } -\value{ -\code{SampleMetadata}: The name of the default assay -} \description{ Get the sample metadata } diff --git a/man/as.AnnData.Rd b/man/as.AnnData.Rd index 91f10270..9ced41cd 100644 --- a/man/as.AnnData.Rd +++ b/man/as.AnnData.Rd @@ -28,9 +28,6 @@ as.AnnData(object, ...) \item{type}{the spatial data type of Seurat object: "image" or "spatial"} } -\value{ -\code{as.AnnData}: The name of the default assay -} \description{ Generic methods for conversion into a AnnData object } diff --git a/man/as.Giotto.Rd b/man/as.Giotto.Rd index c6c2fc41..170d9996 100644 --- a/man/as.Giotto.Rd +++ b/man/as.Giotto.Rd @@ -11,9 +11,6 @@ as.Giotto(object, ...) \item{...}{Arguments passed to other methods} } -\value{ -\code{as.Giotto}: The name of the default assay -} \description{ Generic methods for conversion into a Giotto object } diff --git a/man/as.Seurat.Rd b/man/as.Seurat.Rd index 09b07ae0..25674687 100644 --- a/man/as.Seurat.Rd +++ b/man/as.Seurat.Rd @@ -31,9 +31,6 @@ as.Seurat(object, ...) \item{reg}{if TRUE, registered coordinates will be used} } -\value{ -\code{as.Seurat}: The name of the default assay -} \description{ Generic methods for conversion into a Seurat object } diff --git a/man/as.VoltRon.Rd b/man/as.VoltRon.Rd index c7c98e4c..4d3728c1 100644 --- a/man/as.VoltRon.Rd +++ b/man/as.VoltRon.Rd @@ -18,9 +18,6 @@ as.VoltRon(object, ...) \item{assay_name}{the assay name} } -\value{ -\code{as.VoltRon}: The name of the default assay -} \description{ Generic methods for conversion into a VoltRon object } diff --git a/man/as.Zarr.Rd b/man/as.Zarr.Rd index a89fbfcb..0afb53cc 100644 --- a/man/as.Zarr.Rd +++ b/man/as.Zarr.Rd @@ -21,9 +21,6 @@ as.Zarr(object, out_path, image_id, ...) \item{...}{Arguments passed to other methods} } -\value{ -\code{as.Zarr}: The name of the default assay -} \description{ Generic methods for conversion into a Seurat object } diff --git a/man/changeSampleNames.Rd b/man/changeSampleNames.Rd index aa77c38f..36a00029 100644 --- a/man/changeSampleNames.Rd +++ b/man/changeSampleNames.Rd @@ -21,9 +21,6 @@ changeSampleNames(object, ...) \item{samples}{a single or a set of sample names} } -\value{ -\code{changeSampleNames}: The name of the default assay -} \description{ change sample names of VoltRon or other objects diff --git a/man/flipCoordinates.Rd b/man/flipCoordinates.Rd index e647a580..598b359b 100644 --- a/man/flipCoordinates.Rd +++ b/man/flipCoordinates.Rd @@ -17,9 +17,6 @@ flipCoordinates(object, ...) \item{...}{Arguments passed to other methods} } -\value{ -\code{flipCoordinates}: The name of the default assay -} \description{ Flip the coordinates of the spatial points in the y axis direction } diff --git a/man/getFeatures.Rd b/man/getFeatures.Rd index 9779cb9a..fc8b8260 100644 --- a/man/getFeatures.Rd +++ b/man/getFeatures.Rd @@ -23,9 +23,6 @@ getFeatures(object, ...) \item{n}{the number of features} } -\value{ -Returns object after normalization -} \description{ get spatially variable features in an assay } diff --git a/man/getProfileNeighbors.Rd b/man/getProfileNeighbors.Rd index 92aaf4f4..31b47f49 100644 --- a/man/getProfileNeighbors.Rd +++ b/man/getProfileNeighbors.Rd @@ -35,9 +35,6 @@ getProfileNeighbors(object, ...) \item{graph.key}{the name of the graph} } -\value{ -Returns object after normalization -} \description{ get neighbors in an assay given omic profiles } diff --git a/man/getSpatialNeighbors.Rd b/man/getSpatialNeighbors.Rd index 7aac170d..e04cf3f9 100644 --- a/man/getSpatialNeighbors.Rd +++ b/man/getSpatialNeighbors.Rd @@ -18,9 +18,6 @@ getSpatialNeighbors(object, ...) \item{method}{the method spatial connectivity} } -\value{ -Returns object after normalization -} \description{ get neighbors in an assay given spatial coordinates } diff --git a/man/modulateImage.Rd b/man/modulateImage.Rd index 4a8e5c7c..d735420c 100644 --- a/man/modulateImage.Rd +++ b/man/modulateImage.Rd @@ -23,9 +23,6 @@ modulateImage(object, ...) \item{hue}{modulation of hue is an absolute rotation of -180 degrees to +180 degrees from the current position corresponding to an argument range of 0 to 200 (100 for no change)} } -\value{ -\code{modulateImage}: The name of the default assay -} \description{ Modulating Magick images } diff --git a/man/resizeImage.Rd b/man/resizeImage.Rd index 510b711f..95bd4851 100644 --- a/man/resizeImage.Rd +++ b/man/resizeImage.Rd @@ -19,9 +19,6 @@ resizeImage(object, ...) \item{size}{the width of the resized image} } -\value{ -\code{resizeImage}: The name of the default assay -} \description{ Resizing Magick images } diff --git a/man/vrAssayNames.Rd b/man/vrAssayNames.Rd index 56d69f61..ae9a9d95 100644 --- a/man/vrAssayNames.Rd +++ b/man/vrAssayNames.Rd @@ -27,11 +27,6 @@ vrAssayNames(object, ...) <- value \item{assay}{assay} } -\value{ -\code{vrAssayNames}: The name of the default assay - -\code{vrAssayNames<-}: The coordinates updated -} \description{ Given a VoltRon object, give names of assays of some type, or main assay. } diff --git a/man/vrAssayTypes.Rd b/man/vrAssayTypes.Rd index e104bf33..f3e0f1db 100644 --- a/man/vrAssayTypes.Rd +++ b/man/vrAssayTypes.Rd @@ -19,9 +19,6 @@ vrAssayTypes(object, ...) \item{assay}{assay} } -\value{ -\code{vrAssayTypes}: The name of the default assay -} \description{ Given a VoltRon object, give types of assays of some type, or of the main assay. Here, an assay type is of either cell, spot or ROI. diff --git a/man/vrCoordinates.Rd b/man/vrCoordinates.Rd index 61709603..7212cc47 100644 --- a/man/vrCoordinates.Rd +++ b/man/vrCoordinates.Rd @@ -32,11 +32,6 @@ vrCoordinates(object, ...) <- value \item{assay}{assay} } -\value{ -\code{vrCoordinates}: The name of the default assay - -\code{vrCoordinates<-}: The coordinates updated -} \description{ Get and set the coordinates of the main assay } diff --git a/man/vrData.Rd b/man/vrData.Rd index d1d82162..04771543 100644 --- a/man/vrData.Rd +++ b/man/vrData.Rd @@ -23,9 +23,6 @@ vrData(object, ...) \item{assay}{assay} } -\value{ -\code{vrData}: The name of the default assay -} \description{ Get data from the main.assay } diff --git a/man/vrDistances.Rd b/man/vrDistances.Rd index f370ce05..b860ecb8 100644 --- a/man/vrDistances.Rd +++ b/man/vrDistances.Rd @@ -18,9 +18,6 @@ vrDistances(object, ...) \item{...}{Arguments passed to other methods} } -\value{ -\code{vrDistances}: The name of the default assay -} \description{ Get distances between spatial points using coordinates } diff --git a/man/vrEmbeddingNames.Rd b/man/vrEmbeddingNames.Rd index 92a68eb0..7e4438b6 100644 --- a/man/vrEmbeddingNames.Rd +++ b/man/vrEmbeddingNames.Rd @@ -19,9 +19,6 @@ vrEmbeddingNames(object, ...) \item{assay}{assay} } -\value{ -\code{vrEmbeddingNames}: The name of embeddings -} \description{ Given a VoltRon object, give names of embeddings } diff --git a/man/vrEmbeddings.Rd b/man/vrEmbeddings.Rd index 34589c53..952728cf 100644 --- a/man/vrEmbeddings.Rd +++ b/man/vrEmbeddings.Rd @@ -34,9 +34,6 @@ vrEmbeddings(object, ...) <- value \item{assay}{assay} } -\value{ -\code{vrEmbeddings}: The name of the default assay -} \description{ Get embeddings of spatial points } diff --git a/man/vrFeatureData.Rd b/man/vrFeatureData.Rd index 5b74422b..da0b74ce 100644 --- a/man/vrFeatureData.Rd +++ b/man/vrFeatureData.Rd @@ -30,9 +30,6 @@ vrFeatureData(object, ...) <- value \item{assay}{assay} } -\value{ -\code{vrFeatureData}: The name of the default assay -} \description{ Get and set feature data from the main.assay } diff --git a/man/vrGraph.Rd b/man/vrGraph.Rd index a26ebc1d..b806f25a 100644 --- a/man/vrGraph.Rd +++ b/man/vrGraph.Rd @@ -26,11 +26,6 @@ vrGraph(object, ...) <- value \item{graph.type}{the type of the graph, either custom or given by \code{getProfileNeighbors} or \code{getSpatialNeighbors} functions} } -\value{ -\code{vrGraph}: The name of the default assay - -\code{vrGraph<-}: graph updated -} \description{ Get graph from the main.assay } diff --git a/man/vrGraphNames.Rd b/man/vrGraphNames.Rd index f8c06e48..1b02d418 100644 --- a/man/vrGraphNames.Rd +++ b/man/vrGraphNames.Rd @@ -16,9 +16,6 @@ vrGraphNames(object, ...) \item{assay}{assay} } -\value{ -\code{vrGraphNames}: The names of all graphs -} \description{ Get names of all graphs } diff --git a/man/vrImageNames.Rd b/man/vrImageNames.Rd index 74413873..40e3f309 100644 --- a/man/vrImageNames.Rd +++ b/man/vrImageNames.Rd @@ -19,9 +19,6 @@ vrImageNames(object, ...) \item{assay}{assay} } -\value{ -\code{vrImageNames}: The name of the default assay -} \description{ Get names of all images } diff --git a/man/vrImages.Rd b/man/vrImages.Rd index 9b3d2725..f6570817 100644 --- a/man/vrImages.Rd +++ b/man/vrImages.Rd @@ -37,9 +37,6 @@ vrImages(object, ...) <- value \item{reg}{TRUE if registered coordinates are assigned} } -\value{ -\code{vrImages}: The name of the default assay -} \description{ Get images of a VoltRon assay } diff --git a/man/vrMainAssay.Rd b/man/vrMainAssay.Rd index 1b25db82..051f16f5 100644 --- a/man/vrMainAssay.Rd +++ b/man/vrMainAssay.Rd @@ -22,11 +22,6 @@ vrMainAssay(object, ...) <- value \item{value}{new assay name} } -\value{ -\code{vrMainAssay}: The name of the default assay - -\code{vrMainAssay<-}: The name of the default assay updated -} \description{ Get and set the main assay } diff --git a/man/vrMainImage.Rd b/man/vrMainImage.Rd index a5d2886c..5b1badcd 100644 --- a/man/vrMainImage.Rd +++ b/man/vrMainImage.Rd @@ -22,11 +22,6 @@ vrMainImage(object, ...) <- value \item{value}{the name of main image} } -\value{ -\code{vrMainImage}: The name of the default assay - -\code{vrMainImage}: The name of the default assay -} \description{ Get the main image diff --git a/man/vrSegments.Rd b/man/vrSegments.Rd index c7a1b86b..9fee1bd2 100644 --- a/man/vrSegments.Rd +++ b/man/vrSegments.Rd @@ -32,11 +32,6 @@ vrSegments(object, ...) <- value \item{assay}{assay} } -\value{ -\code{vrSegments}: The name of the default assay - -\code{vrSegments<-}: The coordinates updated -} \description{ Get and set the segments of spatian points of the main assay }