Merge pull request #15 from AlexsLemonade/jashapiro/8-seurat-conversion

Add functions for Seurat conversion

.Rbuildignore

@@ -6,3 +6,4 @@
 ^\.lintr$
 ^\.pre-commit-config.yaml$
 ^data-raw$
+^LICENSE\.md$

.Renviron

@@ -0,0 +1 @@
+RENV_EXT_ENABLED = FALSE

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
         exclude: '\.Rd'
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.28.1
+    rev: v1.28.2
     hooks:
       - id: typos
         exclude: '\.nb\.html'

DESCRIPTION

@@ -21,8 +21,12 @@ LazyData: true
 Suggests:
     testthat (>= 3.0.0),
     scater,
+    scran,
     Seurat,
-    splatter
+    splatter,
+    scuttle,
+    Matrix,
+    SeuratObject
 Config/testthat/edition: 3
 RoxygenNote: 7.3.2
 Imports:
@@ -34,6 +38,7 @@ Imports:
     purrr,
     S4Vectors,
     SingleCellExperiment,
+    SummarizedExperiment,
     tibble,
     tidyr
 biocViews:

LICENSE

@@ -1,28 +1,3 @@
-BSD 3-Clause License
-
-Copyright (c) 2024, Alex's Lemonade Stand Foundation
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+YEAR: 2024
+COPYRIGHT HOLDER: Alex's Lemonade Stand Foundation
+ORGANIZATION: Alex's Lemonade Stand Foundation

LICENSE.md

@@ -0,0 +1,28 @@
+# BSD 3-Clause License
+
+Copyright (c) 2024, Alex's Lemonade Stand Foundation
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NAMESPACE

@@ -6,9 +6,12 @@ export(calculate_silhouette)
 export(calculate_stability)
 export(ensembl_to_symbol)
 export(extract_pc_matrix)
+export(sce_to_seurat)
 export(sce_to_symbols)
+export(sum_duplicate_genes)
 export(sweep_clusters)
 import(SingleCellExperiment)
+import(SummarizedExperiment)
 import(methods)
 importFrom(S4Vectors,`metadata<-`)
 importFrom(S4Vectors,metadata)

R/convert-gene-ids.R

@@ -13,18 +13,21 @@
 #'
 #'
 #' @param ensembl_ids A character vector of Ensembl gene ids to translate to
-#'  gene symbols.
-#' @param reference The reference gene list to use for translation. One of `scpca`,
-#'   `10x2020`, `10x2024`. The `scpca` reference is the default.
-#' @param sce A SingleCellExperiment object to use as a reference for gene symbols.
-#'  If provided, the `reference` argument will be ignored. The `sce` object must
-#'  include columns with the names `gene_ids` (containing Ensembl ids) and
-#'  `gene_symbol` (containing the symbols) to use for conversion.
-#' @param unique Whether to use unique gene symbols, as would be done if
-#'  data had been read in with gene symbols by Seurat. Default is FALSE.
-#' @param leave_na Whether to leave NA values in the output vector.
-#' If FALSE, any missing values will be replaced with the input ensembl_id value.
-#' Default is FALSE.
+#'   gene symbols.
+#' @param reference The reference gene list to use for translation. One of
+#'   `scpca`, `10x2020`, `10x2024`. The `scpca` reference is the default.
+#' @param sce A SingleCellExperiment object to use as a reference for gene
+#'   symbols. If provided, the `reference` argument will be ignored. The `sce`
+#'   object must include columns with the names `gene_ids` (containing Ensembl
+#'   ids) and `gene_symbol` (containing the symbols) to use for conversion.
+#' @param unique Whether to use unique gene symbols, as would be done if data
+#'   had been read in with gene symbols by Seurat. Default is FALSE.
+#' @param leave_na Whether to leave NA values in the output vector. If FALSE,
+#'   any missing values will be replaced with the input ensembl_id value.
+#'   Default is FALSE.
+#' @param seurat_compatible Whether to return a vector that is compatible with
+#'   Seurat, translating and underscores to dashes.
+#'   Default is FALSE.
 #'
 #' @return A vector of gene symbols corresponding to the input Ensembl ids.
 #' @export
@@ -51,7 +54,8 @@ ensembl_to_symbol <- function(
     reference = c("scpca", "10x2020", "10x2024"),
     sce = NULL,
     unique = FALSE,
-    leave_na = FALSE) {
+    leave_na = FALSE,
+    seurat_compatible = FALSE) {
   reference <- match.arg(reference)
   stopifnot(
     "`ensembl_ids` must be a character vector." = is.character(ensembl_ids),
@@ -85,10 +89,17 @@ ensembl_to_symbol <- function(
     )
   }
   if (!leave_na && any(missing_symbols)) {
-    warning("Not all input ids have corresponding gene symbols, using input ids for missing values.")
+    message("Not all input ids have corresponding gene symbols, using input ids for missing values.")
     gene_symbols[missing_symbols] <- ensembl_ids[missing_symbols]
   }
 
+  if (seurat_compatible) {
+    if (any(grepl("_", gene_symbols))) {
+      warning("Replacing underscores ('_') with dashes ('-') in gene symbols for Seurat compatibility.")
+    }
+    gene_symbols <- gsub("_", "-", gene_symbols)
+  }
+
   return(gene_symbols)
 }
 
@@ -112,15 +123,19 @@ ensembl_to_symbol <- function(
 #' (and not disabled by the `convert_hvg` and `convert_pca` arguments).
 #'
 #'
-#' @param sce A SingleCellExperiment object containing gene ids and gene symbols.
-#' @param reference The reference gene list for conversion. One of `sce`, `scpca`,
-#' `10x2020`, or `10x2024`. If `sce` (the default) the internal row data is used.
-#' @param unique Whether to use unique gene symbols, as would be done if
-#' data had been read in with gene symbols by Seurat. Default is FALSE.
-#' @param convert_hvg Logical indicating whether to convert highly variable genes to gene symbols.
-#'  Default is TRUE.
-#' @param convert_pca Logical indicating whether to convert PCA rotation matrix to gene symbols.
-#'  Default is TRUE.
+#' @param sce A SingleCellExperiment object containing gene ids and gene
+#'   symbols.
+#' @param reference The reference gene list for conversion. One of `sce`,
+#'   `scpca`, `10x2020`, or `10x2024`. If `sce` (the default) the internal row
+#'   data is used.
+#' @param unique Whether to use unique gene symbols, as would be done if data
+#'   had been read in with gene symbols by Seurat. Default is FALSE.
+#' @param convert_hvg Logical indicating whether to convert highly variable
+#'   genes to gene symbols. Default is TRUE.
+#' @param convert_pca Logical indicating whether to convert PCA rotation matrix
+#'   to gene symbols. Default is TRUE.
+#' @param seurat_compatible Logical indicating whether to make gene symbols
+#'   Seurat-compatible by replacing underscores with dashes. Default is FALSE.
 #'
 #' @return A SingleCellExperiment object with row names set as gene symbols.
 #' @export
@@ -145,7 +160,8 @@ sce_to_symbols <- function(
     reference = c("sce", "scpca", "10x2020", "10x2024"),
     unique = FALSE,
     convert_hvg = TRUE,
-    convert_pca = TRUE) {
+    convert_pca = TRUE,
+    seurat_compatible = FALSE) {
   reference <- match.arg(reference)
   stopifnot(
     "`sce` must be a SingleCellExperiment object." = is(sce, "SingleCellExperiment"),
@@ -164,9 +180,19 @@ sce_to_symbols <- function(
   }
 
   if (reference == "sce") {
-    gene_symbols <- ensembl_to_symbol(ensembl_ids, sce = sce, unique = unique)
+    gene_symbols <- ensembl_to_symbol(
+      ensembl_ids,
+      sce = sce,
+      unique = unique,
+      seurat_compatible = seurat_compatible
+    )
   } else {
-    gene_symbols <- ensembl_to_symbol(ensembl_ids, reference = reference, unique = unique)
+    gene_symbols <- ensembl_to_symbol(
+      ensembl_ids,
+      reference = reference,
+      unique = unique,
+      seurat_compatible = seurat_compatible
+    )
   }
   row_ids <- gene_symbols
   # set Ensembl ids as original ids for later translations