Bug fixes: plotDimLoadings for only one PC, and allowing DelayedArray in multispati

Author: lambdamoses

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Voyager
 Type: Package
 Title: From geospatial to spatial omics
-Version: 1.9.1
+Version: 1.9.2
 Authors@R: 
     c(person("Lambda", "Moses", email = "[email protected]", 
     role = c("aut", "cre"),
@@ -40,7 +40,7 @@ Imports:
     grid,
     lifecycle,
     Matrix,
-    matrixStats,
+    MatrixGenerics,
     memuse,
     methods,
     patchwork,
@@ -65,12 +65,14 @@ Suggests:
     BiocStyle,
     cowplot,
     data.table,
+    DelayedMatrixStats,
     EBImage,
     ExperimentHub,
     ggh4x,
     gstat,
     hexbin,
     knitr,
+    matrixStats,
     pheatmap,
     RBioFormats,
     rhdf5,

NAMESPACE

@@ -73,6 +73,7 @@ importFrom(DelayedArray,sweep)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
+importFrom(MatrixGenerics,colVars)
 importFrom(RSpectra,eigs_sym)
 importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,"metadata<-")
@@ -194,7 +195,6 @@ importFrom(grid,rasterGrob)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
 importFrom(lifecycle,is_present)
-importFrom(matrixStats,colVars)
 importFrom(memuse,Sys.meminfo)
 importFrom(methods,as)
 importFrom(methods,is)

R/SFEMethod-bivariate.R

@@ -13,7 +13,7 @@
 .lee_mat <- function(x, y = NULL, listw, zero.policy = TRUE, ...) {
     # X has genes in rows
     if (inherits(listw, "listw"))
-        W <- listw2sparse(listw)
+        W <- spatialreg::as_dgRMatrix_listw(listw)
     else W <- listw
     x <- .scale_n(x)
     if (!is.null(y)) {

R/SFEMethod-multivariate.R

@@ -31,7 +31,7 @@
 #' Dray, S., Said, S. and Debias, F. (2008) Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation. Journal of vegetation science, 19, 45-56.
 #' @export
 #' @importFrom Matrix colMeans
-#' @importFrom matrixStats colVars
+#' @importFrom MatrixGenerics colVars
 #' @importFrom utils head tail
 #' @examples
 #' library(SFEData)
@@ -56,12 +56,12 @@ multispati_rsp <- function(x, listw, nfposi = 30L, nfnega = 30L, scale = TRUE) {
     if (scale) {
         # Note that dudi.pca divides by n instead of n-1 when scaling data
         n <- nrow(x)
-        x <- sweep(x, 2, sqrt(matrixStats::colVars(x)*(n-1)/n), FUN = "/")
+        x <- sweep(x, 2, sqrt(colVars(x)*(n-1)/n), FUN = "/")
     }
     if (inherits(listw, "Matrix") || is.matrix(listw))
         W <- listw
     else if (inherits(listw, "listw"))
-        W <- listw2sparse(listw)
+        W <- spatialreg::as_dgRMatrix_listw(listw)
     else
         stop("listw must be either a listw object or an adjacency matrix.")
     covar <- t(x) %*% (W + t(W)) %*% x / (2*nrow(x))

R/plot-non-spatial.R

@@ -117,7 +117,7 @@ ElbowPlot <- function(sce, ndims = 20, nfnega = 0, reduction = "PCA",
 .get_loadings_df <- function(sce, loadings, loading_cols, nfeatures, balanced,
                              swap_rownames) {
     df <- cbind(as.data.frame(rowData(sce)[rownames(loadings),, drop = FALSE]),
-                loadings[, loading_cols])
+                loadings[, loading_cols, drop = FALSE])
     if (is.null(swap_rownames) || !swap_rownames %in% names(df)) {
         df$gene_show <- rownames(loadings)
     } else {

R/spatial-misc.R

@@ -10,7 +10,7 @@
 #' eigenvalues without performing unnecessary work to find the full spectrum as
 #' done in base R's \code{\link{eigen}}.
 #'
-#' @inheritParams SpatialFeatureExperiment::listw2sparse
+#' @param listw A listw object for the spatial neighborhood graph.
 #' @return A numeric vector of minimum and maximum Moran's I given the spatial
 #'   neighborhood graph.
 #' @note
@@ -19,7 +19,7 @@
 #' @export
 #' @importFrom RSpectra eigs_sym
 #' @importFrom spdep listw2mat
-#' @importFrom SpatialFeatureExperiment listw2sparse multi_listw2sparse
+#' @importFrom SpatialFeatureExperiment multi_listw2sparse
 #' @concept Spatial statistics
 #' @references de Jong, P., Sprenger, C., & van Veen, F. (1984). On extreme values of Moran's I and Geary's C. Geographical Analysis, 16(1), 17-24.
 #' @examples

tests/testthat/_snaps/plot/only-plotting-one-pc.svg

@@ -1,5 +1,6 @@
 library(SFEData)
 library(scater)
+library(DelayedArray)
 
 sfe <- McKellarMuscleData("small")
 sfe <- sfe[,sfe$in_tissue]
@@ -61,6 +62,14 @@ test_that("Correct output structure of multispati_rsp, only negative", {
     expect_true(all(eigs < 0))
 })
 
+test_that("multispati_rsp for DelayedArray", {
+    da <- t(DelayedArray(mat))
+    out <- multispati_rsp(da, listw = g, nfposi = 2, nfnega = 2)
+    expect_equal(colnames(out), paste0("PC", 1:4))
+    expect_equal(rownames(out), colnames(sfe))
+    expect_true(is.numeric(out))
+})
+
 ref <- multispati_rsp(t(mat), listw = g, nfposi = 10, nfnega = 10)
 test_that("CalculateMultivariate for matrix", {
     out <- calculateMultivariate(mat, "multispati", listw = g,

tests/testthat/test-multivariate.R

@@ -9,6 +9,8 @@ library(ggplot2)
 library(scran)
 library(EBImage)
 library(scales)
+spdep::set.SubgraphOption(FALSE)
+spdep::set.NoNeighbourOption(FALSE)
 
 expect_ggplot <- function(description, g) {
     expect_s3_class(g, "ggplot")
@@ -467,6 +469,10 @@ test_that("plotDimLoadings for PCA", {
                                         ncol = 1))
 })
 
+test_that("plotDimLoadings, when only plotting one PC", {
+    expect_doppelganger("Only plotting one PC", plotDimLoadings(sfe_muscle, dims = 1))
+})
+
 test_that("plotDimLoadings for multiple samples", {
     expect_doppelganger("Multispati loadings, 2 samples", {
         plotDimLoadings(sfe3, c(1:2, 19:20), swap_rownames = "symbol",