replace Seurat dependency with SeuratObject (#402)

* bump x.y.z version to even y prior to creation of RELEASE_3_18 branch * bump x.y.z version to odd y following creation of RELEASE_3_18 branch * Seurat -> SeuratObject * bump version * test on 3.18 --------- Co-authored-by: J Wokaty <[email protected]>
rnabioco · Nov 7, 2023 · e59930a · e59930a
1 parent df4193c
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,8 +53,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
-          - { os: windows-latest, r: '4.3', bioc: '3.17'}
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
+          - { os: windows-latest, r: '4.3', bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -106,16 +106,16 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -289,7 +289,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
           path: check
 
         ## Note that DOCKER_PASSWORD is really a token for your dockerhub

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: clustifyr
 Title: Classifier for Single-cell RNA-seq Using Cell Clusters
-Version: 1.13.1
+Version: 1.15.1
 Description: Package designed to aid in classifying cells from single-cell RNA sequencing data
     using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A 
     variety of correlation based methods and gene list enrichment methods are provided to assist cell
@@ -73,7 +73,7 @@ Suggests:
     BiocManager,
     remotes,
     shiny,
-    Seurat,
+    SeuratObject,
     gprofiler2,
     purrr,
     data.table,

diff --git a/NAMESPACE b/NAMESPACE
@@ -98,3 +98,4 @@ importFrom(stats,p.adjust)
 importFrom(stats,prcomp)
 importFrom(stats,quantile)
 importFrom(tidyr,gather)
+importFrom(utils,read.csv)
diff --git a/NEWS b/NEWS
@@ -49,4 +49,7 @@ Changes in version 1.5.2 (2021-10-04)
 
 Changes in version 1.7.3 (2022-03-09)
 + `vec_out` option for directly getting classification results as a vector, to be inserted into other metadata/workflow
-+ Maintainer change
++ Maintainer change
+
+Changes in version 1.15.1 (2023-10-31)
++ Replace `Seurat` dependency with `SeuratObject`
diff --git a/R/main.R b/R/main.R
@@ -426,7 +426,7 @@ clustify.Seurat <- function(input,
             }
         }
 
-        if ("Seurat" %in% loadedNamespaces()) {
+        if ("SeuratObject" %in% loadedNamespaces()) {
             s_object <- write_meta(s_object, df_temp_full)
             return(s_object)
         } else {
@@ -917,7 +917,7 @@ clustify_lists.Seurat <- function(input,
             }
         }
 
-        if ("Seurat" %in% loadedNamespaces()) {
+        if ("SeuratObject" %in% loadedNamespaces()) {
             s_object <- write_meta(s_object, df_temp_full)
             return(s_object)
         } else {

diff --git a/R/plot.R b/R/plot.R
@@ -40,13 +40,11 @@ plot_dims <- function(data,
     do_legend = TRUE,
     do_repel = TRUE) {
     # add backticks to allow special characters in column names
-    x_col <- paste0("`", x, "`")
-    y_col <- paste0("`", y, "`")
 
     # If feature is not provided return unlabeled plot
     if (is.null(feature)) {
-        p <- ggplot2::ggplot(data, ggplot2::aes_string(x_col, y_col)) +
-            ggplot2::geom_point(size = pt_size) +
+        p <- ggplot(data, aes(.data[[x]], .data[[y]])) +
+            geom_point(size = pt_size) +
             cowplot::theme_cowplot()
 
         if (!is.null(d_cols)) {
@@ -79,21 +77,17 @@ plot_dims <- function(data,
     data <- dplyr::arrange(data, !!dplyr::sym(feature))
 
     if (!is.null(alpha_col)) {
-        p <- ggplot2::ggplot(data, ggplot2::aes_string(x_col, y_col)) +
-            geom_point(ggplot2::aes_string(
-                color = paste0("`", feature, "`"),
-                alpha = paste0("`", alpha_col, "`")
+        p <- ggplot(data, aes(.data[[x]], .data[[y]])) +
+            geom_point(aes(
+                color = .data[[feature]],
+                alpha = .data[[alpha_col]]
             ), # backticks protect special character gene names
             size = pt_size
             ) +
             scale_alpha_continuous(range = c(0, 1))
     } else {
-        p <- ggplot2::ggplot(data, ggplot2::aes_string(x_col, y_col)) +
-            ggplot2::geom_point(ggplot2::aes_string(color = paste0(
-                "`",
-                feature,
-                "`"
-            )),
+        p <- ggplot(data, aes(.data[[x]], .data[[y]])) +
+            geom_point(aes(color = .data[[feature]]),
             size = pt_size
             )
     }
@@ -177,7 +171,7 @@ plot_dims <- function(data,
             colnames(alldata) <- colnames(centers)
             alldata <- rbind(alldata, centers)
             p <- p +
-                ggplot2::geom_point(
+                geom_point(
                     data = alldata,
                     mapping = aes(
                         x = !!dplyr::sym("t1"),
@@ -200,7 +194,7 @@ plot_dims <- function(data,
                 )
         } else {
             p <- p +
-                ggplot2::geom_text(
+                geom_text(
                     data = centers,
                     mapping = aes(
                         x = !!dplyr::sym("t1"),

diff --git a/R/seurat_wrapper.R b/R/seurat_wrapper.R
@@ -110,12 +110,12 @@ write_meta <- function(object, ...) {
 write_meta.Seurat <- function(object,
     meta,
     ...) {
-    if ("Seurat" %in% loadedNamespaces()) {
+    if ("SeuratObject" %in% loadedNamespaces()) {
         object_new <- object
         object_new@meta.data <- meta
         return(object_new)
     } else {
-        message("Seurat not loaded")
+        message("SeuratObject not loaded")
     }
 }
 

diff --git a/R/utils.R b/R/utils.R
@@ -1000,7 +1000,7 @@ clustify_nudge.Seurat <- function(input,
             rename_prefix = rename_prefix
         )
 
-        if ("Seurat" %in% loadedNamespaces()) {
+        if ("SeuratObject" %in% loadedNamespaces()) {
             input <- write_meta(input, df_temp_full)
             return(input)
         } else {
@@ -1359,6 +1359,7 @@ feature_select_PCA <- function(mat = NULL,
 #'
 #' gene.lists <- gmt_to_list(path = gmt_file)
 #' length(gene.lists)
+#' @importFrom utils read.csv
 #' @export
 gmt_to_list <- function(path,
     cutoff = 0,

diff --git a/README.Rmd b/README.Rmd
@@ -43,8 +43,7 @@ BiocManager::install("clustifyr")
 Install the development version with:
 
 ``` r
-# install.packages("remotes")
-remotes::install_github("rnabioco/clustifyr")
+BiocManager::install("rnabioco/clustifyr")
 ```
 
 ## Example usage

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 coverage](https://codecov.io/gh/rnabioco/clustifyr/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/rnabioco/clustifyr?branch=devel)
 [![platforms](https://bioconductor.org/shields/availability/release/clustifyr.svg)](https://bioconductor.org/packages/release/bioc/html/clustifyr.html)
 [![bioc](https://bioconductor.org/shields/years-in-bioc/clustifyr.svg)](https://bioconductor.org/packages/release/bioc/html/clustifyr.html)
-[![\#downloads](https://img.shields.io/badge/%23%20downloads-7329-brightgreen)](https://bioconductor.org/packages/stats/bioc/clustifyr/clustifyr_stats.tab)
+[![\#downloads](https://img.shields.io/badge/%23%20downloads-8045-brightgreen)](https://bioconductor.org/packages/stats/bioc/clustifyr/clustifyr_stats.tab)
 <!-- badges: end -->
 
 clustifyr classifies cells and clusters in single-cell RNA sequencing
@@ -29,8 +29,7 @@ BiocManager::install("clustifyr")
 Install the development version with:
 
 ``` r
-# install.packages("remotes")
-remotes::install_github("rnabioco/clustifyr")
+BiocManager::install("rnabioco/clustifyr")
 ```
 
 ## Example usage

diff --git a/tests/testthat/test_cor.R b/tests/testthat/test_cor.R
@@ -244,7 +244,7 @@ test_that("clustify reinserts seurat3 metadata correctly", {
         seurat_out = TRUE,
         dr = "tsne"
     )
-    if ("Seurat" %in% loadedNamespaces()) {
+    if ("SeuratObject" %in% loadedNamespaces()) {
         expect_true(class(res) %in% c("Seurat"))
     } else {
         expect_true(is.matrix(res))
@@ -392,7 +392,7 @@ test_that("correct error message is displayed for nonexistent cluster_col", {
 })
 
 test_that("input Seurat metadata columns are not changed (type, r, rn, etc). #259", {
-    skip_if_not_installed("Seurat")
+    skip_if_not_installed("SeuratObject")
     tmp <- s_small3
     tmp@meta.data$type <- 0L
     tmp@meta.data$rn <- 0L

diff --git a/tests/testthat/test_gsea.R b/tests/testthat/test_gsea.R
@@ -1,14 +1,19 @@
 context("run_gsea")
 
+# use capture.output to quiet progress bar from fgsea
+shush <- function(...) {
+  capture.output(..., file = nullfile())
+}
 test_that("output is correctly formatted", {
     data("pbmc_vargenes")
-    res <- run_gsea(
+
+    shush(res <- run_gsea(
         pbmc_matrix_small,
         query_genes = pbmc_vargenes[1:100],
         n_perm = 10,
         cluster_ids = pbmc_meta$classified,
         no_warnings = TRUE
-    )
+    ))
 
     expect_equal(nrow(res), length(unique(pbmc_meta$classified)))
     expect_true(all(res$pval >= 0 & res$pval <= 1))
@@ -30,26 +35,30 @@ test_that("run_gsea checks for matching number of clusters", {
 test_that("run_gsea warns slow runs", {
     data("pbmc_vargenes")
 
-    expect_warning(res <- run_gsea(pbmc_matrix_small[, 1:3],
+    expect_warning(
+      shush(res <- run_gsea(pbmc_matrix_small[, 1:3],
         query_genes = pbmc_vargenes[1:2],
         n_perm = 10001,
         per_cell = TRUE,
         cluster_ids = pbmc_meta$classified,
         no_warnings = TRUE
-    ))
+        )
+      ) 
+    )
 })
 
 test_that("run_gsea warning suppression", {
     data("pbmc_vargenes")
     expect_warning(
-        res <- run_gsea(
+      shush(res <- run_gsea(
             pbmc_matrix_small[, 1:3],
             query_genes = pbmc_vargenes[1:2],
             n_perm = 1,
             per_cell = TRUE,
             cluster_ids = pbmc_meta$classified,
             no_warnings = FALSE
         )
+      ) 
     )
 })
 
@@ -62,7 +71,7 @@ test_that("calculate_pathway_gsea gives appropriate output", {
         pbmc_meta,
         cluster_col = "classified"
     )
-    res <- calculate_pathway_gsea(pbmc_avg, gl, scale = TRUE)
+    shush(res <- calculate_pathway_gsea(pbmc_avg, gl, scale = TRUE))
 
     expect_equal(nrow(res), length(unique(pbmc_meta$classified)))
 })
@@ -76,7 +85,7 @@ test_that("plot_pathway_gsea gives appropriate output", {
         pbmc_meta,
         cluster_col = "classified"
     )
-    g <- plot_pathway_gsea(pbmc_avg, gl, 5)
+    shush(g <- plot_pathway_gsea(pbmc_avg, gl, 5))
     expect_equal(length(g), 2)
 })
 
@@ -89,7 +98,8 @@ test_that("plot_pathway_gsea gives output depending on returning option", {
         pbmc_meta,
         cluster_col = "classified"
     )
-    g <- plot_pathway_gsea(pbmc_avg, gl, 5, returning = "plot")
-    g2 <- plot_pathway_gsea(pbmc_avg, gl, 5, returning = "res")
+    shush(g <- plot_pathway_gsea(pbmc_avg, gl, 5, returning = "plot"))
+    shush(g2 <- plot_pathway_gsea(pbmc_avg, gl, 5, returning = "res"))
+
     expect_true(is(g, "Heatmap") & is.data.frame(g2))
 })