From 2f40d01f461bd9c25eeb3d5520672e1430f104c5 Mon Sep 17 00:00:00 2001
From: Timothy Keyes <tkeyes@stanford.edu>
Date: Mon, 25 Mar 2024 14:30:51 -0700
Subject: [PATCH] update tests/dependencies

---
 DESCRIPTION                           |  5 +++--
 NEWS.md                               | 11 +++++++++++
 tests/testthat/test-quality_control.R | 13 -------------
 3 files changed, 14 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a825b88..f529c85 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidytof
 Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
-Version: 0.99.4
+Version: 0.99.5
 Authors@R: 
     c(person(given = "Timothy",
              family = "Keyes",
@@ -80,7 +80,8 @@ Suggests:
     Seurat,
     SeuratObject,
     embed,
-    rsample
+    rsample,
+    BiocGenerics
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: false
diff --git a/NEWS.md b/NEWS.md
index ab489e5..80b330f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+# tidytof 0.99.5
+
+NEW FEATURES
+
+* Update dependencies. 
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* None
+
 # tidytof 0.99.4
 
 NEW FEATURES
@@ -62,3 +72,4 @@ SIGNIFICANT USER-VISIBLE CHANGES
 BUG FIXES
 
 * None
+
diff --git a/tests/testthat/test-quality_control.R b/tests/testthat/test-quality_control.R
index f3e6565..31f0481 100644
--- a/tests/testthat/test-quality_control.R
+++ b/tests/testthat/test-quality_control.R
@@ -1,10 +1,8 @@
 # libraries
 library(ggplot2)
 library(dplyr)
-library(forcats)
 library(testthat)
 
-
 # tof_assess_channels() --------------------------------------------------------
 
 set.seed(22)
@@ -273,13 +271,6 @@ sim_data <-
         cluster_id = c(rep("a", 1000), rep("b", 1000), rep("c", 1000))
     )
 
-# sim_data |>
-#   tof_reduce_dimensions(method = "pca") |>
-#   tof_plot_cells_embedding(
-#     embedding_cols = c(.pc1, .pc2),
-#     color_col = cluster_id
-#   )
-
 
 sim_data_healthy <-
     sim_data |>
@@ -311,10 +302,6 @@ entropy_result_augmented <-
         augment = TRUE
     )
 
-# entropy_assessment |>
-#   ggplot(aes(x = entropy, fill = cluster_id)) +
-#   geom_density(alpha = 0.4) +
-#   theme_bw()
 
 test_that("Entropy result has the right rows and columns", {
     # rows