Fixed unit tests.

Author: enblacar

R/do_RankedEnrichmentHeatmap.R

@@ -243,6 +243,7 @@ do_RankedEnrichmentHeatmap <- function(sample,
               tidyr::pivot_longer(cols = -dplyr::all_of("Cell"),
                                   names_to = key_col,
                                   values_to = "Score") %>% 
+              dplyr::mutate("{key_col}" := stringr::str_to_upper(.data[[key_col]])) %>% 
               dplyr::filter(.data[[key_col]] %in% vapply(dims, function(x){paste0(key, x)}, FUN.VALUE = character(1))) %>% 
               dplyr::group_by(.data[[key_col]]) %>% 
               dplyr::reframe("rank" = rank(.data$Score),

R/do_RankedExpressionHeatmap.R

@@ -211,6 +211,7 @@ do_RankedExpressionHeatmap <- function(sample,
               tidyr::pivot_longer(cols = -dplyr::all_of("Cell"),
                                   names_to = key_col,
                                   values_to = "Score") %>% 
+              dplyr::mutate("{key_col}" := stringr::str_to_upper(.data[[key_col]])) %>% 
               dplyr::filter(.data[[key_col]] %in% vapply(dims, function(x){paste0(key, x)}, FUN.VALUE = character(1))) %>% 
               dplyr::group_by(.data[[key_col]]) %>% 
               dplyr::reframe("rank" = rank(.data$Score),
@@ -266,7 +267,6 @@ do_RankedExpressionHeatmap <- function(sample,
                  dplyr::mutate("Expression" = ifelse(.data$Expression >= limits[2], limits[2], .data$Expression))
 
     # Compute scale limits, breaks etc.
-    message(limits)
     scale.setup <- compute_scales(sample = NULL,
                                   feature = NULL,
                                   assay = NULL,

R/utils.R

@@ -1274,6 +1274,10 @@ compute_scales <- function(sample,
 
   }
 
+  if (is.na(limits[1]) || is.na(limits[2])) {
+    stop("Invalid axis limits: dmin or dmax is NA.")
+  }
+  
   breaks <- labeling::extended(dmin = limits[1],
                                dmax = limits[2],
                                m = number.breaks)

tests/testthat/test-do_LoadingsHeatmap.R

@@ -35,7 +35,7 @@ if (base::isFALSE(dep_check[["do_LoadingsHeatmap"]])){
 
     p <- SCpubr::do_LoadingsHeatmap(sample = sample,
                                     dims = 1:10,
-                                    max.cutoff.expresion = 0.5)
+                                    max.cutoff.expression = 0.5)
     testthat::expect_true(ggplot2::is_ggplot(p))
 
     p <- SCpubr::do_LoadingsHeatmap(sample = sample,

tests/testthat/test-do_RankedExpressionHeatmap.R

@@ -65,7 +65,7 @@ if (base::isFALSE(dep_check[["do_RankedExpressionHeatmap"]])){
                                             enforce_symmetry = FALSE)
     testthat::expect_type(p, "list")
 
-    testthat::expect_warning({SCpubr::do_RankedExpressionHeatmap(sample = sample,
+    SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                                                  features =  genes,
                                                                  subsample = 100,
                                                                  reduction = "umap",
@@ -74,9 +74,9 @@ if (base::isFALSE(dep_check[["do_RankedExpressionHeatmap"]])){
                                                                  verbose = FALSE,
                                                                  assay = "SCT",
                                                                  use_viridis = FALSE,
-                                                                 enforce_symmetry = FALSE)})
+                                                                 enforce_symmetry = FALSE)
 
-    testthat::expect_warning({SCpubr::do_RankedExpressionHeatmap(sample = sample,
+   SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                                                  features =  genes,
                                                                  subsample = 100,
                                                                  reduction = "umap",
@@ -85,7 +85,7 @@ if (base::isFALSE(dep_check[["do_RankedExpressionHeatmap"]])){
                                                                  verbose = FALSE,
                                                                  slot = "data",
                                                                  use_viridis = FALSE,
-                                                                 enforce_symmetry = FALSE)})
+                                                                 enforce_symmetry = FALSE)
 
     suppressMessages({testthat::expect_message({p <- SCpubr::do_RankedExpressionHeatmap(sample = sample,
                                                                                         features =  genes,