Bugfix percentages in explanatory PC plot

Author: alanocallaghan

DESCRIPTION

@@ -12,8 +12,8 @@ Authors@R: c(
         person("Leo", "Lahti", role=c("ctb"), email="leo.lahti@utu.fi",
 	             comment = c(ORCID = "0000-0001-5537-637X"))
 	)
-Version: 1.31.0
-Date: 2023-08-23
+Version: 1.31.1
+Date: 2023-11-16
 License: GPL-3
 Title: Single-Cell Analysis Toolkit for Gene Expression Data in R
 Description: A collection of tools for doing various analyses of

R/plotExplanatoryPCs.R

@@ -47,9 +47,8 @@ plotExplanatoryPCs <- function(object, nvars_to_plot = 10, npcs_to_plot=50, them
     df_to_plot <- data.frame(
         PC=rep(seq_len(nrow(chosen_rsquared)), ncol(chosen_rsquared)),
         Expl_Var=rep(ordered_vars, each=nrow(chosen_rsquared)),
-        Pct_Var_Explained=as.numeric(chosen_rsquared) * 100 # column major collapse.
+        Pct_Var_Explained=as.numeric(chosen_rsquared) # column major collapse.
     )
-    
     plot_out <- ggplot(df_to_plot, aes(x = .data$PC, y = .data$"Pct_Var_Explained", colour = .data$"Expl_Var")) +
         geom_point(alpha= 1, shape = 16, size = 3) +
         geom_line(alpha = 0.7, linewidth = 2) +

tests/testthat/test-expl-var.R

@@ -151,6 +151,28 @@ test_that("getExplanatoryPCs matches with a reference function", {
     }
 })
 
+
+test_that("getExplanatoryPCs doesn't return more than 100%", {
+    example_sce <- mockSCE()
+    example_sce <- logNormCounts(example_sce)
+    example_sce <- runPCA(example_sce)
+     
+    r2mat <- getExplanatoryPCs(example_sce)
+    expect_true(all(r2mat <= 100))
+})
+
+
+test_that("plotExplanatoryPCs doesn't return more than 100%", {
+    example_sce <- mockSCE()
+    example_sce <- logNormCounts(example_sce)
+    example_sce <- runPCA(example_sce)
+     
+    g <- plotExplanatoryPCs(example_sce)
+    expect_true(all(g$data$Pct_Var_Explained <= 100))
+})
+
+
+
 test_that("getExplanatoryPCs responds to PC-specific options", {
     # Responds to differences in the reduced dimension slot.
     blah <- normed