Fix CHECK

Author: stemangiola

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidybulk
 Title: Brings transcriptomics to the tidyverse 
-Version: 1.99.2
+Version: 1.99.3
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -28,6 +28,7 @@ Imports:
     utils,
     lifecycle,
     scales,
+    ggplot2,
     SummarizedExperiment,
     GenomicRanges,
     methods,
@@ -54,7 +55,6 @@ Suggests:
     Seurat,
     KernSmooth,
     Rtsne,
-    ggplot2,
     widyr,
     clusterProfiler,
     msigdbr,
@@ -95,7 +95,7 @@ RdMacros:
 Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
-LazyData: true
+LazyData: false
 RoxygenNote: 7.3.2
 LazyDataCompression: xz
 URL: https://github.com/stemangiola/tidybulk

R/ggplot.R

@@ -1,7 +1,23 @@
 
+#' Log10 reverse transformation for ggplot2
+#'
+#' Creates a transformation that applies -log10(x) to data, useful for
+#' visualizing p-values or other values where smaller values should be
+#' displayed larger.
+#'
+#' @return A transformation object that can be used with ggplot2's scale functions
+#'
+#' @examples
+#' \dontrun{
+#' library(ggplot2)
+#' # Example usage with p-values
+#' ggplot(data, aes(x = pvalue)) +
+#'   geom_histogram() +
+#'   scale_x_continuous(trans = log10_reverse_trans())
+#' }
+#'
 #' @importFrom scales trans_new
 #' @importFrom scales label_scientific
-#' @noRd
 #' @export
 log10_reverse_trans <- function() {
   trans <- function(x) -log10(x)

R/global_variables.R

@@ -17,6 +17,6 @@ if(getRversion() >= "2.15.1") {
     "ncbi_gene", "fit", "FDR", "constrast", "adj.P.Val", "group_id", 
     "parameter", "CI", "lower", "upper", "term", "sample a", "sample b",
     "abundance", "element", "feature", "rc", "correlation",
-    "buildCustomIdx", "buildIdx", "egsea", "normalize.quantiles"
+    "buildCustomIdx", "buildIdx", "egsea", "normalize.quantiles", "deconvolute", "data_base"
   ))
 } 

man/log10_reverse_trans.Rd

@@ -7,21 +7,30 @@ airway_mini <- airway[1:100, 1:5]
 library(dplyr)
 library(SummarizedExperiment)
 library(tidySummarizedExperiment)
+library(tidybulk)
 library(EGSEA)
 
 # Add entrez and symbol mapping for gene enrichment tests
 if(requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
-  airway_mini <- airway_mini |>
-    mutate(symbol = mapIds(org.Hs.eg.db::org.Hs.eg.db,
-                          keys = .feature,
+  # Get gene names from rownames
+  gene_names <- rownames(airway_mini)
+  
+  # Map gene symbols and entrez IDs
+  symbol_mapping <- mapIds(org.Hs.eg.db::org.Hs.eg.db,
+                          keys = gene_names,
                           keytype = "ENSEMBL",
                           column = "SYMBOL",
-                          multiVals = "first")) |>
-    mutate(entrez = mapIds(org.Hs.eg.db::org.Hs.eg.db,
-                          keys = .feature,
+                          multiVals = "first")
+  
+  entrez_mapping <- mapIds(org.Hs.eg.db::org.Hs.eg.db,
+                          keys = gene_names,
                           keytype = "ENSEMBL",
                           column = "ENTREZID",
-                          multiVals = "first"))
+                          multiVals = "first")
+  
+  # Add mappings to rowData
+  SummarizedExperiment::rowData(airway_mini)$symbol <- symbol_mapping
+  SummarizedExperiment::rowData(airway_mini)$entrez <- entrez_mapping
 }
 
 # Test test_gene_enrichment function

tests/testthat/test-gene-enrichment.R

@@ -1005,7 +1005,7 @@ airway_overrep =
 
 EGSEA [@alhamdoosh2017egsea] is used for ensemble gene set enrichment analysis. EGSEA is a method that combines multiple gene set enrichment analysis methods to provide a more robust and comprehensive analysis of gene set enrichment. It creates a web-based interactive tool that allows you to explore the results of the gene set enrichment analysis.
 
-```{r enrichment-egsea-analysis}
+```{r enrichment-egsea-analysis, eval=FALSE}
 library(EGSEA)
 # Test gene enrichment
   airway |>