update MetadataTable & SampleNames

DESCRIPTION

@@ -28,6 +28,7 @@ Imports:
     leiden (>= 0.4.2),
     markdown (>= 1.1),
     methods (>= 4.1.3),
+    plotly (>= 4.10.0), 
     progressr (>= 0.10.1),
     pryr (>= 0.1.5),
     reshape2 (>= 1.4.4),

R/Metadata_Table.R

@@ -1,9 +1,3 @@
-# This code comes from NIDAP 'Metadata Table [scRNA-seq][CCBR]' code template
-# Template Manager https://nidap.nih.gov/workspace/vector/templates/ri.vector.main.template.6a8139b7-45b4-4c6a-8648-c8ec34e6fc60
-# Documentation https://nidap.nih.gov/workspace/notepad/view/ri.notepad.main.notepad.70a5a28a-fa78-4f77-bee2-30f2d4854304
-# Example https://nidap.nih.gov/workspace/vector/view/ri.vector.main.workbook.d9fbfd7b-fb08-4814-ae16-7327cb7f4f37?branch=master
-
-
 #' @title Extracting meta.data and reductions slots from Seurat-class object
 #' @description Returns the per cell metadata and dimension embeddings (optional) of the Seurat object as a data table.
 #' @details Exposes the metadata of any combined Seurat object, though it is recommended to input a SingleR annotated Seurat Object.
@@ -40,7 +34,8 @@
 
 
 MetadataTable <- function(SO, return.cell.embeddings = FALSE) {
-  # get cell embeddings? ====
+
+  # got cell embeddings? ====
 
   if (return.cell.embeddings) {
     reds = names(SO@reductions)
@@ -72,6 +67,5 @@ MetadataTable <- function(SO, return.cell.embeddings = FALSE) {
 
   # return output ====
 
-  #print(summary(met.df))
   return(met.df)
 }

R/Sample_Names.R

@@ -1,16 +1,11 @@
-# This code comes from NIDAP 'Metadata Table [scRNA-seq][CCBR]' code template https://nidap.nih.gov/workspace/vector/templates/ri.vector.main.template.51ea15ce-2be0-415f-902b-3c86175eb6cd
-# Documentation https://nidap.nih.gov/workspace/notepad/view/ri.notepad.main.notepad.53192624-dba0-4e63-9cbb-9bec776ede47
-# Example https://nidap.nih.gov/workspace/vector/view/ri.vector.main.workbook.00e7a393-4cd7-4f20-bdd2-1c1c0cfd1ea2?branch=master
-
-
-#' Extracting cell identities from the meta.data slot of Seurat-class object
-#' 
 #' Returns tabulation of cell identities present in the orig_ident column
 #' 
 #' It is recommended to run this function after doing SingleR annotations and before doing any visualizations/downstream analysis that requires inputting sample names.
 #' 
 #' @param SO Seurat-class object
 #' 
+#' @importFrom methods slotNames
+#'#' 
 #'   
 #' @export
 #' @return A table (data.frame) with the number of cells per each sample name (column names)

tests/testthat/test-Metadata_Table.R

@@ -1,18 +1,25 @@
+# load data
+seurat.object <-readRDS(test_path("fixtures", "SO_moduleScore.rds"))
 
+
+# run tests
 test_that("reductions are returned", {
 
-  # load data
-  seurat.object <-
-    readRDS(test_path("fixtures", "SO_moduleScore.rds"))
-
-  # run function
   metadata <-
     MetadataTable(SO = seurat.object,
                   return.cell.embeddings = TRUE)
 
-  # test
   expect_true(sum(grepl("PC_1$|PC_2$", colnames(metadata))) == 2)
   expect_true(sum(grepl("UMAP_1|UMAP_2", colnames(metadata))) == 2)
   expect_true(sum(grepl("tSNE_1|tSNE_2", colnames(metadata))) == 2)
 
+})
+
+test_that("function returns correct class", {
+
+  metadata <-
+    MetadataTable(SO = seurat.object,
+                  return.cell.embeddings = TRUE)
+  expect_s3_class(metadata, "data.frame")
+
 })