diff --git a/.Rbuildignore b/.Rbuildignore index a31bf5a3..bb40367f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -16,7 +16,7 @@ ^.*\.h5Seurat$ ^.*\.rds$ ^.*\.Rds$ -^LICENSE$ ^data-raw$ ^inst$ ^tests$ +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 7ebc168d..69b4a601 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: SeuratObject Type: Package Title: Data Structures for Single Cell Data -Version: 4.0.2 -Date: 2021-06-08 +Version: 4.0.3 +Date: 2021-11-10 Authors@R: c( person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')), person(given = 'Andrew', family = 'Butler', email = 'abutler@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')), @@ -26,7 +26,7 @@ URL: https://satijalab.org/seurat, https://github.com/mojaveazure/seurat-object BugReports: https://github.com/mojaveazure/seurat-object/issues -License: GPL-3 +License: MIT + file LICENSE Encoding: UTF-8 LazyData: true RoxygenNote: 7.1.1 diff --git a/LICENSE b/LICENSE index f288702d..4b479715 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,2 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. +YEAR: 2021 +COPYRIGHT HOLDER: SeuratObject authors diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 00000000..a8d2091f --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +# MIT License + +Copyright (c) 2021 SeuratObject authors + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/NAMESPACE b/NAMESPACE index e13d1596..a2e8775d 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -157,15 +157,18 @@ export(Assays) export(AttachDeps) export(Cells) export(CellsByIdentities) +export(CheckDots) export(CheckGC) export(Command) export(CreateAssayObject) export(CreateDimReducObject) export(CreateSeuratObject) export(DefaultAssay) +export(DefaultDimReduc) export(Distances) export(Embeddings) export(FetchData) +export(FilterObjects) export(GetAssayData) export(GetImage) export(GetTissueCoordinates) @@ -185,8 +188,10 @@ export(Loadings) export(LogSeuratCommand) export(Misc) export(Neighbors) +export(PackageCheck) export(Project) export(Radius) +export(RandomName) export(Reductions) export(RenameAssays) export(RenameCells) diff --git a/NEWS.md b/NEWS.md index 651b8a93..e528b2c9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# SeuratObject 4.0.3 + +## Changed +- Export utility functions (#22) +- Bug fix in names with `Key.Seurat` (#26) +- Improved duplicate key checking and resolution + # SeuratObject 4.0.2 ## Changed @@ -15,7 +22,7 @@ - Allow super classes to replace child classes (#1). For example, allows `Assay` objects to replace `Seurat::SCTAssay` or `Signac::ChromatinAssay` objects of the same name -- Better support for creating sparse matrices from `data.table`/`tibble` +- Better support for creating sparse matrices from `data.table`/`tibble` objects (#4) - Improved error messages for clashing object names (#7) - Allow returning a `NULL` if a subset results in zero cells (#9) diff --git a/R/seurat.R b/R/seurat.R index 142c2eab..e4e16add 100644 --- a/R/seurat.R +++ b/R/seurat.R @@ -499,6 +499,52 @@ FetchData <- function(object, vars, cells = NULL, slot = 'data') { return(data.fetched) } +#' Find Sub-objects of a Certain Class +#' +#' Get the names of objects within a \code{Seurat} object that are of a +#' certain class +#' +#' @param object A \code{\link{Seurat}} object +#' @param classes.keep A vector of names of classes to get +#' +#' @return A vector with the names of objects within the \code{Seurat} object +#' that are of class \code{classes.keep} +#' +#' @export +#' +#' @examples +#' FilterObjects(pbmc_small) +#' +FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) { + object <- UpdateSlots(object = object) + slots <- na.omit(object = Filter( + f = function(x) { + sobj <- slot(object = object, name = x) + return(is.list(x = sobj) && !is.data.frame(x = sobj) && !is.package_version(x = sobj)) + }, + x = slotNames(x = object) + )) + slots <- grep(pattern = 'tools', x = slots, value = TRUE, invert = TRUE) + slots <- grep(pattern = 'misc', x = slots, value = TRUE, invert = TRUE) + slots.objects <- unlist( + x = lapply( + X = slots, + FUN = function(x) { + return(names(x = slot(object = object, name = x))) + } + ), + use.names = FALSE + ) + object.classes <- sapply( + X = slots.objects, + FUN = function(i) { + return(inherits(x = object[[i]], what = classes.keep)) + } + ) + object.classes <- which(x = object.classes, useNames = TRUE) + return(names(x = object.classes)) +} + #' @rdname ObjectAccess #' @export #' @@ -1313,12 +1359,16 @@ Key.Seurat <- function(object, ...) { object = object, classes.keep = c('Assay', 'DimReduc', 'SpatialImage') ) - return(sapply( + keys <- vapply( X = keyed.objects, FUN = function(x) { return(Key(object = object[[x]])) - } - )) + }, + FUN.VALUE = character(length = 1L), + USE.NAMES = FALSE + ) + names(x = keys) <- keyed.objects + return(keys) } #' @param reduction Name of reduction to pull feature loadings for @@ -2766,30 +2816,43 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes } Key(object = value) <- UpdateKey(key = Key(object = value)) # Check for duplicate keys - object.keys <- sapply( - X = FilterObjects(object = x), - FUN = function(i) { - return(Key(object = x[[i]])) - } - ) - if (Key(object = value) %in% object.keys && is.null(x = FindObject(object = x, name = i))) { - # Attempt to create a duplicate key based off the name of the object being added - new.keys <- c(paste0(tolower(x = i), c('_', paste0(RandomName(length = 2L), '_')))) - # Select new key to use - key.use <- min(which(x = !new.keys %in% object.keys)) - new.key <- if (is.infinite(x = key.use)) { - RandomName(length = 17L) + object.keys <- Key(object = x) + vkey <- Key(object = value) + if (vkey %in% object.keys && !isTRUE(x = object.keys[i] == vkey)) { + new.key <- if (is.na(x = object.keys[i])) { + # Attempt to create a duplicate key based off the name of the object being added + new.keys <- paste0( + paste0(tolower(x = i), c('', RandomName(length = 2L))), + '_' + ) + # Select new key to use + key.use <- min(which(x = !new.keys %in% object.keys)) + new.key <- if (is.infinite(x = key.use)) { + RandomName(length = 17L) + } else { + new.keys[key.use] + } + warning( + "Cannot add objects with duplicate keys (offending key: ", + Key(object = value), + "), setting key to '", + new.key, + "'", + call. = FALSE + ) + new.key } else { - new.keys[key.use] + # Use existing key + warning( + "Cannot add objects with duplicate keys (offending key: ", + Key(object = value), + ") setting key to original value '", + object.keys[i], + "'", + call. = FALSE + ) + object.keys[i] } - warning( - "Cannot add objects with duplicate keys (offending key: ", - Key(object = value), - "), setting key to '", - new.key, - "'", - call. = FALSE - ) # Set new key Key(object = value) <- new.key } @@ -2797,7 +2860,7 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes # For Assays, run CalcN if (inherits(x = value, what = 'Assay')) { if ((!i %in% Assays(object = x)) | - (i %in% Assays(object = x) && ! identical( + (i %in% Assays(object = x) && !identical( x = GetAssayData(object = x, assay = i, slot = "counts"), y = GetAssayData(object = value, slot = "counts")) )) { @@ -3082,48 +3145,6 @@ DefaultImage <- function(object) { return(images[[1]]) } -#' Get the names of objects within a Seurat object that are of a certain class -#' -#' @param object A \code{\link{Seurat}} object -#' @param classes.keep A vector of names of classes to get -#' -#' @return A vector with the names of objects within the Seurat object that are -#' of class \code{classes.keep} -#' -#' @keywords internal -#' -#' @noRd -#' -FilterObjects <- function(object, classes.keep = c('Assay', 'DimReduc')) { - object <- UpdateSlots(object = object) - slots <- na.omit(object = Filter( - f = function(x) { - sobj <- slot(object = object, name = x) - return(is.list(x = sobj) && !is.data.frame(x = sobj) && !is.package_version(x = sobj)) - }, - x = slotNames(x = object) - )) - slots <- grep(pattern = 'tools', x = slots, value = TRUE, invert = TRUE) - slots <- grep(pattern = 'misc', x = slots, value = TRUE, invert = TRUE) - slots.objects <- unlist( - x = lapply( - X = slots, - FUN = function(x) { - return(names(x = slot(object = object, name = x))) - } - ), - use.names = FALSE - ) - object.classes <- sapply( - X = slots.objects, - FUN = function(i) { - return(inherits(x = object[[i]], what = classes.keep)) - } - ) - object.classes <- which(x = object.classes, useNames = TRUE) - return(names(x = object.classes)) -} - #' Find the collection of an object within a Seurat object #' #' @param object A \code{\link{Seurat}} object diff --git a/R/utils.R b/R/utils.R index 43a08659..5bcf6f8b 100644 --- a/R/utils.R +++ b/R/utils.R @@ -156,6 +156,67 @@ CheckGC <- function(option = 'SeuratObject.memsafe') { return(invisible(x = NULL)) } +#' Find the default \code{\link{DimReduc}} +#' +#' Searches for \code{\link{DimReduc}s} matching \dQuote{umap}, \dQuote{tsne}, +#' or \dQuote{pca}, case-insensitive, and in that order. Priority given to +#' \code{\link{DimReduc}s} matching the \code{DefaultAssay} or assay specified +#' (eg. \dQuote{pca} for the default assay weights higher than \dQuote{umap} +#' for a non-default assay) +#' +#' @param object A \code{\link{Seurat}} object +#' @param assay Name of assay to use; defaults to the default assay of the object +#' +#' @return The default \code{\link{DimReduc}}, if possible +#' +#' @export +#' +#' @examples +#' DefaultDimReduc(pbmc_small) +#' +DefaultDimReduc <- function(object, assay = NULL) { + object <- UpdateSlots(object = object) + assay <- assay %||% DefaultAssay(object = object) + drs.use <- c('umap', 'tsne', 'pca') + dim.reducs <- FilterObjects(object = object, classes.keep = 'DimReduc') + drs.assay <- Filter( + f = function(x) { + return(DefaultAssay(object = object[[x]]) == assay) + }, + x = dim.reducs + ) + if (length(x = drs.assay) > 0) { + index <- lapply( + X = drs.use, + FUN = grep, + x = drs.assay, + ignore.case = TRUE + ) + index <- Filter(f = length, x = index) + if (length(x = index) > 0) { + return(drs.assay[min(index[[1]])]) + } + } + index <- lapply( + X = drs.use, + FUN = grep, + x = dim.reducs, + ignore.case = TRUE + ) + index <- Filter(f = length, x = index) + if (length(x = index) < 1) { + stop( + "Unable to find a DimReduc matching one of '", + paste(drs.use[1:(length(x = drs.use) - 1)], collapse = "', '"), + "', or '", + drs.use[length(x = drs.use)], + "', please specify a dimensional reduction to use", + call. = FALSE + ) + } + return(dim.reducs[min(index[[1]])]) +} + #' Check if a matrix is empty #' #' Takes a matrix and asks if it's empty (either 0x0 or 1x1 with a value of NA) @@ -232,6 +293,60 @@ ListToS4 <- function(x) { return(do.call(what = new, args = c(list(Class = formal), x))) } +#' Check the existence of a package +#' +#' @param ... Package names +#' @param error If true, throw an error if the package doesn't exist +#' +#' @return Invisibly returns boolean denoting if the package is installed +#' +#' @export +#' +#' @examples +#' PackageCheck("SeuratObject", error = FALSE) +#' +PackageCheck <- function(..., error = TRUE) { + pkgs <- unlist(x = c(...), use.names = FALSE) + package.installed <- vapply( + X = pkgs, + FUN = requireNamespace, + FUN.VALUE = logical(length = 1L), + quietly = TRUE + ) + if (error && any(!package.installed)) { + stop( + "Cannot find the following packages: ", + paste(pkgs[!package.installed], collapse = ', '), + ". Please install" + ) + } + invisible(x = package.installed) +} + +#' Generate a random name +#' +#' Make a name from randomly sampled lowercase letters, pasted together with no +#' spaces or other characters +#' +#' @param length How long should the name be +#' @param ... Extra parameters passed to \code{\link[base]{sample}} +#' +#' @return A character with \code{nchar == length} of randomly sampled letters +#' +#' @seealso \code{\link[base]{sample}} +#' +#' @export +#' +#' @examples +#' set.seed(42L) +#' RandomName() +#' RandomName(7L, replace = TRUE) +#' +RandomName <- function(length = 5L, ...) { + CheckDots(..., fxns = 'sample') + return(paste(sample(x = letters, size = length, ...), collapse = '')) +} + #' Merge Sparse Matrices by Row #' #' Merge two or more sparse matrices by rowname. @@ -373,18 +488,47 @@ S4ToList.list <- function(object) { # Internal #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -#' Check the use of dots +#' Check the Use of Dots +#' +#' Function to check the use of unused arguments passed to \code{...}; this +#' function is designed to be called from another function to see if an +#' argument passed to \code{...} remains unused and alert the user if so. Also +#' accepts a vector of function or function names to see if \code{...} can be +#' used in a downstream function +#' +#' Behavior of \code{CheckDots} can be controlled by the following option(s): +#' \describe{ +#' \item{\dQuote{\code{Seurat.checkdots}}}{Control how to alert the presence +#' of unused arguments in \code{...}; choose from +#' \itemize{ +#' \item \dQuote{\code{warn}}: emit a warning (default) +#' \item \dQuote{\code{error}}: throw an error +#' \item \dQuote{\code{silent}}: no not alert the presence of unused +#' arguments in \code{...} +#' } +#' } +#' } #' #' @param ... Arguments passed to a function that fall under \code{...} #' @param fxns A list/vector of functions or function names #' -#' @return ... +#' @return Emits either an error or warning if an argument passed is unused; +#' invisibly returns \code{NULL} #' #' @importFrom utils isS3stdGeneric methods argsAnywhere isS3method #' #' @keywords internal #' -#' @noRd +#' @export +#' +#' @examples +#' \dontrun{ +#' f <- function(x, ...) { +#' CheckDots(...) +#' return(x ^ 2) +#' } +#' f(x = 3, y = 9) +#' } #' CheckDots <- function(..., fxns = NULL) { args.names <- names(x = list(...)) @@ -513,6 +657,7 @@ CheckDots <- function(..., fxns = NULL) { # } } } + return(invisible(x = NULL)) } #' Check a list of objects for duplicate cell names @@ -606,34 +751,6 @@ IsNullPtr <- function(x) { return(.Call('isnull', x)) } -#' Generate a random name -#' -#' Make a name from randomly sampled lowercase letters, pasted together with no -#' spaces or other characters -#' -#' @param length How long should the name be -#' @param ... Extra parameters passed to \code{\link[base]{sample}} -#' -#' @return A character with \code{nchar == length} of randomly sampled letters -#' -#' @seealso \code{\link[base]{sample}} -#' -#' @keywords internal -#' -#' @noRd -#' -#' @examples -#' \dontrun{ -#' set.seed(42L) -#' SeuratObject:::RandomName() -#' SeuratObject:::RandomName(7L, replace = TRUE) -#' } -#' -RandomName <- function(length = 5L, ...) { - CheckDots(..., fxns = 'sample') - return(paste(sample(x = letters, size = length, ...), collapse = '')) -} - #' Update a Class's Package #' #' Swap packages for an object's class definition. As classes move between diff --git a/cran-comments.md b/cran-comments.md index e74cc7ba..f47e03b0 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,7 @@ -# SeuratObject v4.0.2 +# SeuratObject v4.0.3 ## Test environments -* local ubuntu 20.04 install, R 4.0.5 -* local macOS 10.14.6 install, R 4.0.5 +* local ubuntu 20.04 install, R 4.1.1 * win-builder (release, devel) ## R CMD check results @@ -11,4 +10,8 @@ There were no ERRORs, WARNINGs, or NOTEs ## Downstream dependencies -There are two packages that import SeuratObject; this update does impact their functionality. There are two packages that suggest SeuratObject; this update does not impact their functionality. +There is one package that depends on SeuratObject: tidyseurat; this update does not impact its functionality + +There are three packages that import SeuratObject: Platypus, Seurat, and Singac; this update does not impact their functionality + +There are two packages that suggest SeuratObject: singleCellHaystack and VAM; this update does not impact their functionality diff --git a/man/CheckDots.Rd b/man/CheckDots.Rd new file mode 100644 index 00000000..20e3f469 --- /dev/null +++ b/man/CheckDots.Rd @@ -0,0 +1,49 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{CheckDots} +\alias{CheckDots} +\title{Check the Use of Dots} +\usage{ +CheckDots(..., fxns = NULL) +} +\arguments{ +\item{...}{Arguments passed to a function that fall under \code{...}} + +\item{fxns}{A list/vector of functions or function names} +} +\value{ +Emits either an error or warning if an argument passed is unused; +invisibly returns \code{NULL} +} +\description{ +Function to check the use of unused arguments passed to \code{...}; this +function is designed to be called from another function to see if an +argument passed to \code{...} remains unused and alert the user if so. Also +accepts a vector of function or function names to see if \code{...} can be +used in a downstream function +} +\details{ +Behavior of \code{CheckDots} can be controlled by the following option(s): +\describe{ + \item{\dQuote{\code{Seurat.checkdots}}}{Control how to alert the presence + of unused arguments in \code{...}; choose from + \itemize{ + \item \dQuote{\code{warn}}: emit a warning (default) + \item \dQuote{\code{error}}: throw an error + \item \dQuote{\code{silent}}: no not alert the presence of unused + arguments in \code{...} + } + } +} +} +\examples{ +\dontrun{ +f <- function(x, ...) { + CheckDots(...) + return(x ^ 2) +} +f(x = 3, y = 9) +} + +} +\keyword{internal} diff --git a/man/DefaultDimReduc.Rd b/man/DefaultDimReduc.Rd new file mode 100644 index 00000000..757eb15a --- /dev/null +++ b/man/DefaultDimReduc.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{DefaultDimReduc} +\alias{DefaultDimReduc} +\title{Find the default \code{\link{DimReduc}}} +\usage{ +DefaultDimReduc(object, assay = NULL) +} +\arguments{ +\item{object}{A \code{\link{Seurat}} object} + +\item{assay}{Name of assay to use; defaults to the default assay of the object} +} +\value{ +The default \code{\link{DimReduc}}, if possible +} +\description{ +Searches for \code{\link{DimReduc}s} matching \dQuote{umap}, \dQuote{tsne}, +or \dQuote{pca}, case-insensitive, and in that order. Priority given to +\code{\link{DimReduc}s} matching the \code{DefaultAssay} or assay specified +(eg. \dQuote{pca} for the default assay weights higher than \dQuote{umap} +for a non-default assay) +} +\examples{ +DefaultDimReduc(pbmc_small) + +} diff --git a/man/FilterObjects.Rd b/man/FilterObjects.Rd new file mode 100644 index 00000000..f0ee8406 --- /dev/null +++ b/man/FilterObjects.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/seurat.R +\name{FilterObjects} +\alias{FilterObjects} +\title{Find Sub-objects of a Certain Class} +\usage{ +FilterObjects(object, classes.keep = c("Assay", "DimReduc")) +} +\arguments{ +\item{object}{A \code{\link{Seurat}} object} + +\item{classes.keep}{A vector of names of classes to get} +} +\value{ +A vector with the names of objects within the \code{Seurat} object +that are of class \code{classes.keep} +} +\description{ +Get the names of objects within a \code{Seurat} object that are of a +certain class +} +\examples{ +FilterObjects(pbmc_small) + +} diff --git a/man/PackageCheck.Rd b/man/PackageCheck.Rd new file mode 100644 index 00000000..be9fd4c3 --- /dev/null +++ b/man/PackageCheck.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{PackageCheck} +\alias{PackageCheck} +\title{Check the existence of a package} +\usage{ +PackageCheck(..., error = TRUE) +} +\arguments{ +\item{...}{Package names} + +\item{error}{If true, throw an error if the package doesn't exist} +} +\value{ +Invisibly returns boolean denoting if the package is installed +} +\description{ +Check the existence of a package +} +\examples{ +PackageCheck("SeuratObject", error = FALSE) + +} diff --git a/man/RandomName.Rd b/man/RandomName.Rd new file mode 100644 index 00000000..9aa17822 --- /dev/null +++ b/man/RandomName.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{RandomName} +\alias{RandomName} +\title{Generate a random name} +\usage{ +RandomName(length = 5L, ...) +} +\arguments{ +\item{length}{How long should the name be} + +\item{...}{Extra parameters passed to \code{\link[base]{sample}}} +} +\value{ +A character with \code{nchar == length} of randomly sampled letters +} +\description{ +Make a name from randomly sampled lowercase letters, pasted together with no +spaces or other characters +} +\examples{ +set.seed(42L) +RandomName() +RandomName(7L, replace = TRUE) + +} +\seealso{ +\code{\link[base]{sample}} +} diff --git a/man/SeuratObject-package.Rd b/man/SeuratObject-package.Rd index 7048921d..a3936dee 100644 --- a/man/SeuratObject-package.Rd +++ b/man/SeuratObject-package.Rd @@ -25,7 +25,7 @@ Useful links: } \author{ -\strong{Maintainer}: Paul Hoffman \email{nygcSatijalab@nygenome.org} (\href{https://orcid.org/0000-0002-7693-8957}{ORCID}) +\strong{Maintainer}: Paul Hoffman \email{seurat@nygenome.org} (\href{https://orcid.org/0000-0002-7693-8957}{ORCID}) Authors: \itemize{