data.table oriented workflow

DESCRIPTION

@@ -24,8 +24,12 @@ Depends:
 Imports:
     data.table (>= 1.12.8),
     flashpcaR (>= 2.1),
+    fs (>= 1.4.1),
+    ggforce (>= 0.3.2),
     ggplot2 (>= 3.3.2),
-    gt (>= 0.2.1)
+    ggtext (>= 0.1.0),
+    gt (>= 0.2.1),
+    patchwork (>= 1.0.1)
 Suggests:
     roxygen2 (>= 7.1.0)
 Remotes: 

NAMESPACE

@@ -6,3 +6,4 @@ export(pca_report)
 import(data.table)
 import(ggplot2)
 import(gt)
+import(patchwork)

NEWS.md

@@ -1,9 +1,13 @@
 # rain (development version)
 
-## Breaking CHanges
+## Breaking Changes
 
 * In `R/pca_report.R`,
-    + Code refactoring.
+    + Code refactoring using `data.table`.
+* In `R/compute_pca.R`,
+    + Code refactoring using `data.table`.
+    + Tweak ethnicity figure.
+    + Add an ethnicity figure focussing on the studied cohort.
 
 # rain 0.4.1
 

R/check_bin.R

@@ -6,18 +6,17 @@
 check_bin <- function(bin_path) {
   if (!all(sapply(bin_path, file.exists))) {
     message_prefix <- "[rain] "
+    text <- paste0(
+      names(bin_path[!sapply(bin_path, file.exists)]),
+      ' ("', bin_path[!sapply(bin_path, file.exists)], '")'
+    )
     stop(
       message_prefix,
       paste0(
         "No binary found for the following tools: ",
-        glue::glue_collapse(
-          x = paste0(
-            names(bin_path[!sapply(bin_path, file.exists)]),
-            ' ("', bin_path[!sapply(bin_path, file.exists)], '")'
-          ),
-          sep = ", ",
-          last = " and "
-        ),
+        paste(text[-length(text)], collapse = ", "),
+        " and ",
+        text[length(text)],
         "!"
       )
     )