Merge pull request #304 from mvfki/newObj

Back to "rliger"
welch-lab · Mar 14, 2024 · e23c66e · e23c66e
2 parents 530b137 + 4e70862
commit e23c66e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: rliger2
+Package: rliger
 Version: 1.99.0
 Date: 2023-11-09
 Type: Package
@@ -37,7 +37,7 @@ LazyData: true
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
-LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
+LinkingTo: Rcpp, RcppArmadillo, RcppProgress
 Depends:
     methods,
     stats,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,8 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("$",liger)
+S3method("$<-",liger)
 S3method("[",liger)
 S3method("[",ligerDataset)
 S3method("[[",liger)
+S3method("[[<-",liger)
+S3method("names<-",liger)
 S3method(.DollarNames,liger)
 S3method(as.liger,Seurat)
 S3method(as.liger,SingleCellExperiment)
@@ -15,6 +19,9 @@ S3method(as.ligerDataset,matrix)
 S3method(c,liger)
 S3method(cbind,ligerDataset)
 S3method(fortify,liger)
+S3method(length,liger)
+S3method(lengths,liger)
+S3method(names,liger)
 S3method(normalize,Seurat)
 S3method(normalize,dgCMatrix)
 S3method(normalize,liger)
@@ -85,6 +92,7 @@ export(importBMMC)
 export(importCGE)
 export(importPBMC)
 export(imputeKNN)
+export(is.newLiger)
 export(isH5Liger)
 export(ligerATACDataset)
 export(ligerCommand)
@@ -191,8 +199,6 @@ exportClasses(ligerDataset)
 exportClasses(ligerMethDataset)
 exportClasses(ligerRNADataset)
 exportClasses(ligerSpatialDataset)
-exportMethods("$")
-exportMethods("$<-")
 exportMethods("cellMeta<-")
 exportMethods("coordinate<-")
 exportMethods("dataset<-")
@@ -203,7 +209,6 @@ exportMethods("dimRed<-")
 exportMethods("dimnames<-")
 exportMethods("featureMeta<-")
 exportMethods("h5fileInfo<-")
-exportMethods("names<-")
 exportMethods("normData<-")
 exportMethods("normPeak<-")
 exportMethods("rawData<-")
@@ -226,8 +231,6 @@ exportMethods(featureMeta)
 exportMethods(getH5File)
 exportMethods(getMatrix)
 exportMethods(h5fileInfo)
-exportMethods(length)
-exportMethods(names)
 exportMethods(normData)
 exportMethods(normPeak)
 exportMethods(rawData)
@@ -253,4 +256,4 @@ importFrom(methods,show)
 importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(utils,.DollarNames)
-useDynLib(rliger2, .registration = TRUE)
+useDynLib(rliger, .registration = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-## rliger2 1.9.9
+## rliger 1.9.9
 
 - Added `ligerDataset` class for per-dataset information storage, with inheritance for specific modalities
 - Added a number of plotting functions with clear function names and useful functionality
@@ -12,7 +12,7 @@
 Now named by `runINMF()`, `runUINMF()` and `runOnlineINMF()` respectively, and wrapped in 
 `runIntegration()`.
 
-## rliger2 1.0.1
+## rliger 1.0.1
 
 - Allow setting mito pattern in `getMitoProportion()` #271
 - Fix efficiency issue when taking the log of norm.data (e.g. `runWilcoxon`)

diff --git a/R/ATAC.R b/R/ATAC.R
@@ -16,7 +16,7 @@
 #' @param scale Logical. Whether to scale but not center the imputed data.
 #' Default \code{TRUE}.
 #' @param verbose Logical. Whether to show information of the progress. Default
-#' \code{getOption("ligerVerbose")} which is \code{TRUE} if users have not set.
+#' \code{getOption("ligerVerbose")} or \code{TRUE} if users have not set.
 #' @param ... Optional arguments to be passed to \code{\link{normalize}} when
 #' \code{norm = TRUE}.
 #' @param knn_k \bold{Deprecated}. See Usage section for replacement.
@@ -44,7 +44,7 @@ imputeKNN <- function(
         weight = TRUE,
         norm = TRUE,
         scale = FALSE,
-        verbose = getOption("ligerVerbose"),
+        verbose = getOption("ligerVerbose", TRUE),
         ...,
         # Deprecated coding style,
         knn_k = nNeighbors
@@ -152,7 +152,7 @@ imputeKNN <- function(
 #' Peak-gene correlations with p-values below this threshold are considered
 #' significant. Default \code{0.05}.
 #' @param verbose Logical. Whether to show information of the progress. Default
-#' \code{getOption("ligerVerbose")} which is \code{TRUE} if users have not set.
+#' \code{getOption("ligerVerbose")} or \code{TRUE} if users have not set.
 #' @param path_to_coords,genes.list,dist \bold{Deprecated}. See Usage section
 #' for replacement.
 #' @return A sparse matrix with peak names as rows and gene names as columns,
@@ -171,7 +171,7 @@ imputeKNN <- function(
 #'     bmmc <- imputeKNN(bmmc, reference = "atac", queries = "rna")
 #'     corr <- linkGenesAndPeaks(
 #'         bmmc, useDataset = "rna",
-#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger2")
+#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger")
 #'     )
 #' }
 linkGenesAndPeaks <- function(
@@ -181,7 +181,7 @@ linkGenesAndPeaks <- function(
         useGenes = NULL,
         method = c("spearman", "pearson", "kendall"),
         alpha = 0.05,
-        verbose = getOption("ligerVerbose"),
+        verbose = getOption("ligerVerbose", TRUE),
         # Deprecated coding style
         path_to_coords = pathToCoords,
         genes.list = useGenes,
@@ -359,12 +359,12 @@ linkGenesAndPeaks <- function(
 #'     bmmc <- imputeKNN(bmmc, reference = "atac", queries = "rna")
 #'     corr <- linkGenesAndPeaks(
 #'         bmmc, useDataset = "rna",
-#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger2")
+#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger")
 #'     )
 #'     resultPath <- tempfile()
 #'     exportInteractTrack(
 #'         corrMat = corr,
-#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger2"),
+#'         pathToCoords = system.file("extdata/hg19_genes.bed", package = "rliger"),
 #'         outputPath = resultPath
 #'     )
 #'     head(read.table(resultPath, skip = 1))
@@ -478,10 +478,10 @@ exportInteractTrack <- function(
 #' current working directory.
 #' @return No return value. A file located at \code{outputPath} will be created.
 #' @name makeInteractTrack-deprecated
-#' @seealso \code{\link{rliger2-deprecated}}, \code{\link{exportInteractTrack}}
+#' @seealso \code{\link{rliger-deprecated}}, \code{\link{exportInteractTrack}}
 NULL
 
-#' @rdname rliger2-deprecated
+#' @rdname rliger-deprecated
 #' @section \code{makeInteractTrack}:
 #' For \code{makeInteractTrack}, use \code{\link{exportInteractTrack}}.
 #' @export

diff --git a/R/DEG_marker.R b/R/DEG_marker.R
@@ -40,7 +40,7 @@
 #' @param seed Random seed to use for pseudo-replicate generation. Default
 #' \code{1}.
 #' @param verbose Logical. Whether to show information of the progress. Default
-#' \code{getOption("ligerVerbose")} which is \code{TRUE} if users have not set.
+#' \code{getOption("ligerVerbose")} or \code{TRUE} if users have not set.
 #' @return A data.frame with DEG information
 #' @rdname liger-DEG
 #' @export
@@ -65,7 +65,7 @@ runPairwiseDEG <- function(
         nPsdRep = 5,
         minCellPerRep = 10,
         seed = 1,
-        verbose = getOption("ligerVerbose")
+        verbose = getOption("ligerVerbose", TRUE)
 ) {
     method <- match.arg(method)
     if (is.null(variable1) && is.null(variable2)) {
@@ -155,7 +155,7 @@ runMarkerDEG <- function(
         nPsdRep = 5,
         minCellPerRep = 10,
         seed = 1,
-        verbose = getOption("ligerVerbose")
+        verbose = getOption("ligerVerbose", TRUE)
 ) {
     useDatasets <- .checkUseDatasets(object, useDatasets)
     allCellIdx <- seq(ncol(object))[object$dataset %in% useDatasets]
@@ -237,7 +237,7 @@ runWilcoxon <- function(
         nPsdRep = 5,
         minCellPerRep = 10,
         seed = 1,
-        verbose = getOption("ligerVerbose")
+        verbose = getOption("ligerVerbose", TRUE)
 ) {
     method <- match.arg(method)
     allCellIdx <- unlist(groups)
@@ -381,7 +381,7 @@ makePseudoBulk <- function(mat, replicateAnn, minCellPerRep, verbose = TRUE) {
 }
 
 .callDESeq2 <- function(pseudoBulks, groups,
-                         verbose = getOption("ligerVerbose")) {
+                         verbose = getOption("ligerVerbose", TRUE)) {
     # DESeq2 workflow
     if (isTRUE(verbose)) cliID <- cli::cli_process_start("Calling DESeq2 Wald test")
     ## NOTE: DESeq2 wishes that the contrast/control group is the first level

diff --git a/R/DoubletFinder.R b/R/DoubletFinder.R
@@ -20,7 +20,7 @@
 #' @param nExp The total number of doublet predictions produced. Scalar for all
 #' used datasets or vector for each. Default \code{NULL} sets a 0.15 proportion.
 #' @param verbose Logical. Whether to show information of the progress. Default
-#' \code{getOption("ligerVerbose")} which is \code{TRUE} if users have not set.
+#' \code{getOption("ligerVerbose")} or \code{TRUE} if users have not set.
 #' @param ... Additional arguments passed to
 #' \code{DoubletFinder::doubletFinder}.
 #' @return Updated \code{object} with variables \code{DoubletFinder_pANN} and
@@ -37,7 +37,7 @@ runDoubletFinder <- function(
         PCs = 1:10,
         nNeighbors = 20,
         nExp = NULL,
-        verbose = getOption("ligerVerbose"),
+        verbose = getOption("ligerVerbose", TRUE),
         ...
 ) {
     if (!requireNamespace("DoubletFinder", quietly = TRUE)) { # nocov start

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -2,55 +2,55 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 RunModularityClusteringCpp <- function(SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename) {
-    .Call(`_rliger2_RunModularityClusteringCpp`, SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
+    .Call(`_rliger_RunModularityClusteringCpp`, SNN, modularityFunction, resolution, algorithm, nRandomStarts, nIterations, randomSeed, printOutput, edgefilename)
 }
 
 colNormalize_dense_cpp <- function(x, L) {
-    .Call(`_rliger2_colNormalize_dense_cpp`, x, L)
+    .Call(`_rliger_colNormalize_dense_cpp`, x, L)
 }
 
 colAggregateMedian_dense_cpp <- function(x, group, n) {
-    .Call(`_rliger2_colAggregateMedian_dense_cpp`, x, group, n)
+    .Call(`_rliger_colAggregateMedian_dense_cpp`, x, group, n)
 }
 
 scaleNotCenter_byRow_rcpp <- function(x) {
-    .Call(`_rliger2_scaleNotCenter_byRow_rcpp`, x)
+    .Call(`_rliger_scaleNotCenter_byRow_rcpp`, x)
 }
 
 scaleNotCenter_byRow_perDataset_rcpp <- function(x, ann, n) {
-    .Call(`_rliger2_scaleNotCenter_byRow_perDataset_rcpp`, x, ann, n)
+    .Call(`_rliger_scaleNotCenter_byRow_perDataset_rcpp`, x, ann, n)
 }
 
 rowVars_sparse_rcpp <- function(x, means) {
-    .Call(`_rliger2_rowVars_sparse_rcpp`, x, means)
+    .Call(`_rliger_rowVars_sparse_rcpp`, x, means)
 }
 
 rowDivide_rcpp <- function(x, v) {
-    .Call(`_rliger2_rowDivide_rcpp`, x, v)
+    .Call(`_rliger_rowDivide_rcpp`, x, v)
 }
 
 sumSquaredDeviations <- function(x, means) {
-    .Call(`_rliger2_sumSquaredDeviations`, x, means)
+    .Call(`_rliger_sumSquaredDeviations`, x, means)
 }
 
 denseZScore <- function(x, m) {
-    .Call(`_rliger2_denseZScore`, x, m)
+    .Call(`_rliger_denseZScore`, x, m)
 }
 
 rowVarsDense <- function(x, m) {
-    .Call(`_rliger2_rowVarsDense`, x, m)
+    .Call(`_rliger_rowVarsDense`, x, m)
 }
 
 SparseRowVarStd <- function(x, mu, sd, vmax) {
-    .Call(`_rliger2_SparseRowVarStd`, x, mu, sd, vmax)
+    .Call(`_rliger_SparseRowVarStd`, x, mu, sd, vmax)
 }
 
 colAggregateSums_sparse <- function(x, group, ngroups) {
-    .Call(`_rliger2_colAggregateSums_sparse`, x, group, ngroups)
+    .Call(`_rliger_colAggregateSums_sparse`, x, group, ngroups)
 }
 
 sample_cpp <- function(x, size) {
-    .Call(`_rliger2_sample_cpp`, x, size)
+    .Call(`_rliger_sample_cpp`, x, size)
 }
 
 #' Fast calculation of feature count matrix
@@ -68,46 +68,46 @@ sample_cpp <- function(x, size) {
 #' samnple <- gene.counts + promoter.counts
 #' }
 makeFeatureMatrix <- function(bedmat, barcodes) {
-    .Call(`_rliger2_makeFeatureMatrix`, bedmat, barcodes)
+    .Call(`_rliger_makeFeatureMatrix`, bedmat, barcodes)
 }
 
 cluster_vote_rcpp <- function(nn_ranked, clusts) {
-    .Call(`_rliger2_cluster_vote_rcpp`, nn_ranked, clusts)
+    .Call(`_rliger_cluster_vote_rcpp`, nn_ranked, clusts)
 }
 
 max_factor_rcpp <- function(H, dims_use, center = FALSE) {
-    .Call(`_rliger2_max_factor_rcpp`, H, dims_use, center)
+    .Call(`_rliger_max_factor_rcpp`, H, dims_use, center)
 }
 
-ComputeSNN <- function(nn_ranked, prune) {
-    .Call(`_rliger2_ComputeSNN`, nn_ranked, prune)
+ComputeSNN <- function(nn_idx, prune) {
+    .Call(`_rliger_ComputeSNN`, nn_idx, prune)
 }
 
 WriteEdgeFile <- function(snn, filename, display_progress) {
-    invisible(.Call(`_rliger2_WriteEdgeFile`, snn, filename, display_progress))
+    invisible(.Call(`_rliger_WriteEdgeFile`, snn, filename, display_progress))
 }
 
 DirectSNNToFile <- function(nn_ranked, prune, display_progress, filename) {
-    .Call(`_rliger2_DirectSNNToFile`, nn_ranked, prune, display_progress, filename)
+    .Call(`_rliger_DirectSNNToFile`, nn_ranked, prune, display_progress, filename)
 }
 
 cpp_rank_matrix_dgc <- function(x, p, nrow, ncol) {
-    .Call(`_rliger2_cpp_rank_matrix_dgc`, x, p, nrow, ncol)
+    .Call(`_rliger_cpp_rank_matrix_dgc`, x, p, nrow, ncol)
 }
 
 rowAggregateSum_sparse <- function(X, groups, ngroups) {
-    .Call(`_rliger2_rowAggregateSum_sparse`, X, groups, ngroups)
+    .Call(`_rliger_rowAggregateSum_sparse`, X, groups, ngroups)
 }
 
 colAggregateSum_sparse <- function(X, groups, ngroups) {
-    .Call(`_rliger2_colAggregateSum_sparse`, X, groups, ngroups)
+    .Call(`_rliger_colAggregateSum_sparse`, X, groups, ngroups)
 }
 
 colNNZAggr_sparse <- function(X, groups, ngroups) {
-    .Call(`_rliger2_colNNZAggr_sparse`, X, groups, ngroups)
+    .Call(`_rliger_colNNZAggr_sparse`, X, groups, ngroups)
 }
 
 rowNNZAggr_sparse <- function(X, groups, ngroups) {
-    .Call(`_rliger2_rowNNZAggr_sparse`, X, groups, ngroups)
+    .Call(`_rliger_rowNNZAggr_sparse`, X, groups, ngroups)
 }
 
diff --git a/R/aaa.R b/R/aaa.R
@@ -3,7 +3,7 @@
 #' @importFrom rlang .data %||%
 #' @importFrom methods new show
 #' @importFrom utils .DollarNames
-#' @useDynLib rliger2, .registration = TRUE
+#' @useDynLib rliger, .registration = TRUE
 NULL
 
 #' @importFrom magrittr %>%
@@ -75,6 +75,6 @@ scPalette <- c('#E41A1C', '#377EB8', '#4DAF4A', '#FFCF00', '#aa47b9', '#e67c14',
 }
 
 .onUnload <- function(libpath) {
-    library.dynam.unload("rliger2", libpath)
+    library.dynam.unload("rliger", libpath)
     return(invisible(NULL))
 }