adds dplyr to suggests

metamaden · Jul 19, 2023 · 5b8d972 · 5b8d972
1 parent 893c9d2
commit 5b8d972
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Showing 4 changed files with 7 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,17 +12,17 @@ URL: https://github.com/metamaden/lute
 BugReports: https://github.com/metamaden/lute/issues
 LazyData: FALSE
 Depends:
-    R (>= 3.5.0),
+    R (>= 4.2),
     SummarizedExperiment,
     SingleCellExperiment,
     Biobase,
     S4Vectors
 Imports:
-    dplyr,
     methods,
-    nnls,
     stats
 Suggests:
+    nnls, 
+    dplyr,
     glmnet,
     knitr,
     testthat,

diff --git a/R/lute_classes.R b/R/lute_classes.R
@@ -33,7 +33,7 @@ setClass("cellProportionsPredictions", slots = c(predictions.table = "data.frame
 cellProportionsPredictions <- function(predictions.table, 
                                        cell.type.vector = NULL, 
                                        sample.id.vector = NULL) {
-  requireNamespace("dplyr")
+  library(dplyr)
   if(is(cell.type.vector, "NULL")){
     cell.type.vector <- colnames(predictions.table) 
   }

diff --git a/R/lute_utilities.R b/R/lute_utilities.R
@@ -39,7 +39,7 @@
 ypb_from_sce <- function(sce, assay.name = "counts", 
                          celltype.variable = "celltype", 
                          sample.id.variable = NULL, S = NULL){
-  requireNamespace("dplyr")
+  library(dplyr)
   num.groups <- 1; unique.group.id.vector <- ""
   if(!is(sample.id.variable, "NULL")){
     group.id.vector <- sce[[sample.id.variable]]
@@ -99,7 +99,7 @@ signature_matrix_from_sce <- function(sce,
                                       celltype.variable = "celltype", 
                                       summary.method = "mean", 
                                       assay.name = "counts"){
-  requireNamespace("dplyr")
+  library(dplyr)
   # gets the z signature matrix from an sce object
   expression.matrix <- assays(sce)[[assay.name]] %>% as.matrix()
   cd <- colData(sce)
@@ -262,7 +262,7 @@ signature_matrix_from_sce <- function(sce,
 .parse_deconvolution_predictions_results <- function(list.pred, 
                                                      column.labels, 
                                                      row.labels){
-  requireNamespace("dplyr")
+  library(dplyr)
   table.pred <- do.call(rbind, list.pred)
   table.pred <- apply(table.pred, 1, function(ri){ri/sum(ri)}) %>% t()
   colnames(table.pred) <- column.labels

diff --git a/vignettes/lute_users_guide.Rmd b/vignettes/lute_users_guide.Rmd
@@ -16,7 +16,6 @@ output:
     toc_depth: 0
 vignette: > 
   %\VignetteIndexEntry{The lute user's guide}
-  %\VignetteDepends{RCurl}
   %\usepackage[UTF-8]{inputenc} 
   %\VignetteEncoding{UTF-8}
   %\VignetteEngine{knitr::rmarkdown}