From 395f5afff996cbad674e3b23d7d3e360967041e8 Mon Sep 17 00:00:00 2001
From: Stu Field <stu.g.field@gmail.com>
Date: Tue, 19 Sep 2023 16:47:17 -0600
Subject: [PATCH] Make `.refactorData()` less chatty when unnecessary

---
 R/plotPDFbyGroup.R  | 3 +--
 R/plotVolcanoHTML.R | 4 +---
 R/utils.R           | 9 +++------
 3 files changed, 5 insertions(+), 11 deletions(-)

diff --git a/R/plotPDFbyGroup.R b/R/plotPDFbyGroup.R
index 1c3fd6f..5492b08 100644
--- a/R/plotPDFbyGroup.R
+++ b/R/plotPDFbyGroup.R
@@ -71,8 +71,7 @@ plotPDFbyGroup <- function(data, apt, group.var, cols, xlim = NULL,
   p <- data |>
     dplyr::select(!!group.var, apt) |>
     .refactorData() |>     # this is about ghost levels
-    ggplot(aes(x = !!sym(apt),
-               color = !!group.var)) +
+    ggplot(aes(x = !!sym(apt), color = !!group.var)) +
     geom_density(aes(fill  = !!group_var),
                  alpha = ifelse(fill, 0.2, 1),
                  linewidth = ifelse(fill, 0.1, 0.75),
diff --git a/R/plotVolcanoHTML.R b/R/plotVolcanoHTML.R
index d844682..383dc3f 100644
--- a/R/plotVolcanoHTML.R
+++ b/R/plotVolcanoHTML.R
@@ -93,9 +93,7 @@ plotVolcanoHTML.default <- function(data, ...) {
 #'   variable name in `data` for the Target Names.
 #' @importFrom SomaDataIO rn2col col2rn
 #' @export
-plotVolcanoHTML.data.frame <- function(data,
-                                       FC = signed.log2.fold.change,
-                                       p.vec = p.value,
+plotVolcanoHTML.data.frame <- function(data, FC = signed.log2.fold.change, p.vec = p.value,
                                        cutoff = 0.05 / nrow(data),
                                        fc.cutoff = 1,
                                        main = NULL, x.lab = NULL,
diff --git a/R/utils.R b/R/utils.R
index 7a1ff4c..4678d8f 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -54,13 +54,10 @@
   for ( meta in nms ) {
     levs <- levels(data[[meta]])
     data[[meta]] <- droplevels(data[[meta]])
-    if ( interactive() ) {
-      levs2 <- levels(data[[meta]])
+    sdiff <- setdiff(levs, levels(data[[meta]]))
+    if ( length(sdiff) > 0L && interactive() ) {
       .info(
-        paste("Dropping levels",
-              value(setdiff(levs, levs2)),
-              "from",
-              value(meta))
+        paste("Dropping levels", value(sdiff), "from", value(meta))
       )
     }
   }