Adding spelling check and testthat

DESCRIPTION

@@ -5,7 +5,7 @@ Date: 2023-9-15
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"))
 Description: Implementation of the Ibex algorithm for single-cell embedding based on BCR sequences. The package includes a standalone function to encode BCR sequence information by amino acid properties or sequence order using tensorflow-based autoencoder. In addition, the package interacts with SingleCellExperiment or Seurat data objects. 
-License: MIT
+License: MIT + file LICENSE 
 Encoding: UTF-8
 LazyData: true
 LazyDataCompression: xz
@@ -35,5 +35,10 @@ Suggests:
 	viridis,
 	patchwork,
 	ggplot2,
-	harmony
+	harmony,
+	spelling,
+        testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Language: en-US
+URL: /~https://github.com/ncborcherding/Ibex/
+BugReports: /~https://github.com/ncborcherding/Ibex/issues

R/CoNGAfy.R

@@ -16,7 +16,7 @@
 #' clonotype group.
 #' @param features Selected genes for the reduction DEFAULT: null will return all genes
 #' @param assay The name of the assay or assays to return.
-#' @param meta.carry Variables to carry over from the meta data of thje single-cell object
+#' @param meta.carry Variables to carry over from the meta data of the single-cell object
 #' 
 #' @export
 #' @importFrom SeuratObject CreateSeuratObject CreateAssayObject

R/ibex_example.R

@@ -1,5 +1,5 @@
-#' A seurat object of 315 single B cells in
-#' human tonisls
+#' A seurat object of 370 single B cells in
+#' multisystem inflammatory syndrome
 #' @name ibex_example
 #' @docType data
 #'

README.md

@@ -83,7 +83,7 @@ seuratObj <- RunUMAP(seuratObj, reduction = "Ibex",  reduction.key = "Ibex_")
 
 If using Seurat package, the Ibex embedding information and gene expression PCA can be used to find the [Weighted Nearest Neighbors](https://pubmed.ncbi.nlm.nih.gov/34062119/). Before applying the WNN approach, best practice would be to remove the BCR-related genes from the list of variable genes and rerunning the PCA analysis. 
 
-### Recaluclate PCA without BCR genes with queitBCRgenes() function in Ibex.
+### Recalculate PCA without BCR genes with quietBCRgenes() function in Ibex.
 ```r
 seuratObj <- quietBCRgenes(seuratObj)
 seuratObj <- RunPCA(seuratObj)

inst/WORDLIST

@@ -0,0 +1,56 @@
+ADT
+AE
+Atchley
+Autoencoded
+Autoencoder
+BCR
+BCRs
+BLOSUM
+Biorxiv
+CMD
+COVID
+CoNGA
+Codecov
+Experiemt
+Ig
+KF
+Kidera
+OHE
+Satija's
+SingleCell
+SingleCellExperiment
+TCR
+Trex
+UMAP
+VAE
+WNN
+aaReduction
+autoencoded
+autoencoder
+autoencoders
+cdr
+clonality
+clonotype
+clonotypes
+combineBCR
+customizable
+distReduction
+geomteric
+github
+https
+keras
+multisystem
+ncbi
+nih
+nlm
+preprint
+pubmed
+quietBCRgenes
+runIbex
+scRepertoire
+scran
+seurat
+tSNE
+tensorflow
+variational
+vectorize

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
+library(testthat)
+library(Ibex)
+
+test_check("Ibex")

tests/testthat/helper-testingFunctions.R

@@ -0,0 +1,3 @@
+getdata <- function(dir, name) {
+	readRDS(paste("testdata/", dir, "/", name, ".rds", sep = "")) # could move testdata 1 dir lvl up nstead
+}

tests/testthat/test-runIbex.R

@@ -0,0 +1,43 @@
+# test script for runTrex.R - testcases are NOT comprehensive!
+
+test_that("runIbex works with seurat objects", {
+	data("ibex_example")
+  set.seed(42)
+
+  ibex_example <- runIbex(ibex_example, 
+                          chains = "Heavy",
+                          method = "encoder",
+                          encoder.model = "VAE",
+                          encoder.input = "AF", 
+                          reduction.name = "Heavy_VAE_AF")
+
+	expect_equal(
+		ibex_example@reductions$Heavy_VAE_AF@cell.embeddings,
+		getdata("runIbex", "runIbex_Heavy_VAE_AF_reduction")
+	)
+
+	ibex_example <- runIbex(ibex_example, 
+	                        chains = "Light",
+	                        method = "encoder",
+	                        encoder.model = "AE",
+	                        encoder.input = "KF", 
+	                        reduction.name = "Light_AE_KF")
+
+	expect_equal(
+	  ibex_example@reductions$Light_AE_KF@cell.embeddings,
+	  getdata("runIbex", "runIbex_Light_AE_KF_reduction")
+	)
+
+	ibex_example <- runIbex(ibex_example, 
+	                        chains = "Heavy",
+	                        method = "encoder",
+	                        encoder.model = "VAE",
+	                        encoder.input = "OHE", 
+	                        reduction.name = "Heavy_VAE_OHE")
+
+	expect_equal(
+	  ibex_example@reductions$Heavy_VAE_OHE@cell.embeddings,
+	  getdata("runIbex", "runIbex_Heavy_VAE_OHE_reduction")
+	)
+
+})