diff --git a/DESCRIPTION b/DESCRIPTION index 11e2f0b7..aafe2866 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rliger Version: 2.0.1 -Date: 2024-03-24 +Date: 2024-04-04 Type: Package Title: Linked Inference of Genomic Experimental Relationships Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) , and Liu J, Gao C, Sodicoff J, et al (2020) for more details. @@ -37,7 +37,7 @@ LazyData: true RoxygenNote: 7.3.1 VignetteBuilder: knitr Encoding: UTF-8 -Additional_repositories: https:/welch-lab.r-universe.dev, https://blaserlab.r-universe.dev +Additional_repositories: https://welch-lab.r-universe.dev, https://blaserlab.r-universe.dev LinkingTo: Rcpp, RcppArmadillo, RcppProgress Depends: methods, diff --git a/NAMESPACE b/NAMESPACE index 69f7d8b3..870d8c14 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -52,6 +52,7 @@ S3method(writeH5,default) S3method(writeH5,dgCMatrix) S3method(writeH5,liger) S3method(writeH5,ligerDataset) +export("%<>%") export("%>%") export("cellMeta<-") export("coordinate<-") @@ -266,6 +267,7 @@ importFrom(Matrix,summary) importFrom(Matrix,t) importFrom(Rcpp,evalCpp) importFrom(ggplot2,fortify) +importFrom(magrittr,"%<>%") importFrom(magrittr,"%>%") importFrom(methods,new) importFrom(methods,show) diff --git a/NEWS.md b/NEWS.md index 7049700c..ea880d21 100644 --- a/NEWS.md +++ b/NEWS.md @@ -17,7 +17,7 @@ - Fixed wrong UINMF aborting criteria - Fixed example/test skipping criteria for non-existing dependencies -- Fixed file access issue when checking package on CRAN +- Fixed file access issue when checking on CRAN - Updated installed data file `system.file("extdata/ctrl.h5", "extdata/stim.h5")` to be of standard 10X H5 format - Updated `quantileNorm()` automatic reference selection according to #297 - Other minor fixes (including #308) diff --git a/R/aaa.R b/R/aaa.R index a407ac10..458c38e9 100644 --- a/R/aaa.R +++ b/R/aaa.R @@ -10,6 +10,10 @@ NULL #' @export magrittr::`%>%` +#' @importFrom magrittr %<>% +#' @export +magrittr::`%<>%` + scPalette <- c('#E41A1C', '#377EB8', '#4DAF4A', '#FFCF00', '#aa47b9', '#e67c14', '#e7a2b4', '#54B0E4', '#9a5831', '#BC9DCC', '#222F75', '#1B9E77', '#B2DF8A', '#E3BE00', '#FF6699', '#8f3c4d', '#01e1e6', '#591cc5', diff --git a/R/import.R b/R/import.R index 346921fa..a2377dfd 100644 --- a/R/import.R +++ b/R/import.R @@ -445,7 +445,7 @@ createH5LigerDataset <- function( #' # Save and read regular current-version liger object #' tempPath <- tempfile(fileext = ".rds") #' saveRDS(pbmc, tempPath) -#' pbmc <- readLiger(tempPath) +#' pbmc <- readLiger(tempPath, dimredName = NULL) #' #' # Save and read H5-based liger object #' h5Path <- system.file("extdata/ctrl.h5", package = "rliger") diff --git a/data/bmmc.rda b/data/bmmc.rda index 8e66429a..476f5172 100644 Binary files a/data/bmmc.rda and b/data/bmmc.rda differ diff --git a/data/pbmc.rda b/data/pbmc.rda index 2d6beece..5dfe9ff3 100644 Binary files a/data/pbmc.rda and b/data/pbmc.rda differ diff --git a/data/pbmcPlot.rda b/data/pbmcPlot.rda index c4f32caa..1c7ffc64 100644 Binary files a/data/pbmcPlot.rda and b/data/pbmcPlot.rda differ diff --git a/man/readLiger.Rd b/man/readLiger.Rd index 0982412d..1402d2ed 100644 --- a/man/readLiger.Rd +++ b/man/readLiger.Rd @@ -45,7 +45,7 @@ structure by default. # Save and read regular current-version liger object tempPath <- tempfile(fileext = ".rds") saveRDS(pbmc, tempPath) -pbmc <- readLiger(tempPath) +pbmc <- readLiger(tempPath, dimredName = NULL) # Save and read H5-based liger object h5Path <- system.file("extdata/ctrl.h5", package = "rliger") diff --git a/man/reexports.Rd b/man/reexports.Rd index 68970992..254e6023 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -4,6 +4,7 @@ \name{reexports} \alias{reexports} \alias{\%>\%} +\alias{\%<>\%} \title{Objects exported from other packages} \keyword{internal} \description{ @@ -11,6 +12,6 @@ These objects are imported from other packages. Follow the links below to see their documentation. \describe{ - \item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}} + \item{magrittr}{\code{\link[magrittr:compound]{\%<>\%}}, \code{\link[magrittr:pipe]{\%>\%}}} }}