fix & quiet test warnings

.Rbuildignore

@@ -1,10 +1,20 @@
-^requirements\.txt$
+# Github and docs
+^\.github$
+^CONTRIBUTING\.md$
+
+# user settings
+^.*\.Rproj$
+^\.Rproj\.user$
+
+# renv files
 ^renv$
 ^renv\.lock$
 ^dependencies\.R$
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.github$
-^README\.Rmd$
+^requirements\.txt$
+^\.venv$
+
+# rendered notebooks
 ^inst/rmd/.*\.html$
+
+# Docker folder
 ^docker$

.github/workflows/build-docker.yaml

@@ -16,7 +16,7 @@ env:
 
 jobs:
   build_and_push:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     permissions:
       contents: read
       packages: write

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scpcaTools
 Type: Package
 Title: Single cell data tools for ScPCA
-Version: 0.2.3
+Version: 0.3.0
 Authors@R: c(
     person("Ally", "Hawkins",
            email = "[email protected]",
@@ -27,10 +27,10 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
 Depends:
-    R (>= 4.2.0)
+    R (>= 4.3.0)
 Imports:
     BiocGenerics,
-    bluster,
+    bluster (>= 1.10),
     dplyr,
     DropletUtils,
     fishpond,
@@ -39,7 +39,7 @@ Imports:
     jsonlite,
     Matrix,
     methods,
-    miQC (>= 1.2.0),
+    miQC,
     purrr,
     rlang,
     S4Vectors,
@@ -66,6 +66,5 @@ Suggests:
     testthat (>= 3.0.0),
     zellkonverter
 Remotes:
-    AlexsLemonade/scpcaData,
-    github::immunogenomics/lisi
+    AlexsLemonade/scpcaData
 Config/testthat/edition: 3

R/calculate_ilisi.R

@@ -12,6 +12,7 @@
 #'  is a normalized version if `ilisi_score` where values range from [0,1], inclusive
 #'
 #' @import SingleCellExperiment
+#' @importFrom rlang .data
 #'
 #' @export
 calculate_ilisi <- function(merged_sce,
@@ -52,17 +53,17 @@ calculate_ilisi <- function(merged_sce,
   ilisi_df <- lisi::compute_lisi(
     labeled_pcs,
     # define the batches
-    batch_df,
+    meta_data = batch_df,
     # which variables in `batch_df` to compute lisi for
-    "batch"
+    label_colnames = "batch"
   ) |>
-    dplyr::rename(ilisi_score = batch) |>
+    dplyr::rename("ilisi_score" = "batch") |>
     dplyr::mutate(
       cell_barcode = rownames(labeled_pcs),
       batch_id = batch_df$batch,
       # add normalized iLISI score as in in scib approach:
       # https://github.com/theislab/scib/blob/067eb1aee7044f5ce0652fa363ec8deab0e9668d/scib/metrics/lisi.py#L98-L100
-      ilisi_score_norm = (ilisi_score - 1)/(num_batches - 1)
+      ilisi_score_norm = (.data$ilisi_score - 1)/(num_batches - 1)
     )
 
   # Return data frame with cell-wise iLISI scores and associated cell & batch identifiers

R/integrate_sces.R

@@ -148,7 +148,7 @@ integrate_fastmnn <- function(merged_sce,
 #'   being integrated.
 #' @param covariate_cols A vector of other columns to consider as
 #'   covariates during integration.
-#' @param ... Additional arguments to pass into `harmony::harmonyMatrix()`
+#' @param ... Additional arguments to pass into `harmony::HarmonyMatrix()`
 #'
 #' @return Integrated PCs as calculated by `harmony`
 #'
@@ -183,6 +183,7 @@ integrate_harmony <- function(merged_sce,
   harmony_results <- harmony::HarmonyMatrix(reducedDim(merged_sce, "PCA"),
     meta_data = harmony_metadata,
     vars_use  = covariate_cols,
+    verbose = FALSE,
     ...
   )
   # Ensure PCs have rownames

tests/testthat/test-collapse_intron_counts.R

@@ -65,9 +65,9 @@ test_that("Check spliced collapse", {
   )
 })
 
-test_that("Check unspliced collapse", {
-  collapsed_mat <- collapse_intron_counts(intron_mat, "unspliced")
-  collapsed_usa <- collapse_intron_counts(usa_mat, "unspliced")
+test_that("Check total(unspliced) collapse", {
+  collapsed_mat <- collapse_intron_counts(intron_mat, "total")
+  collapsed_usa <- collapse_intron_counts(usa_mat, "total")
   # check the contents
   expect_equal(
     collapsed_mat@x,