Fix typo on example for registration_wrapper(). Add a bit more about …

…how to explore the results. Actually with k = 2 we can run the pairwise model, so I've re-enabled that. Updating the warning for k = 2 accordingly. Used RStudio's automatic code formatter + styler's addin for styling the active file. Re-ran devtools::document(). Related to #86.
LieberInstitute · Oct 22, 2024 · f2ccc25 · f2ccc25
1 parent 9b1c722
commit f2ccc25
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Showing 3 changed files with 66 additions and 53 deletions.
diff --git a/R/registration_wrapper.R b/R/registration_wrapper.R
@@ -47,13 +47,19 @@
 #' ## Compute all modeling results
 #' example_modeling_results <- registration_wrapper(
 #'     sce,
-#'     var_regustration ="Cell_Cycle", 
-#'     var_sample_id ="sample_id", 
+#'     var_registration = "Cell_Cycle",
+#'     var_sample_id = "sample_id",
 #'     covars = c("age"),
-#'     gene_ensembl = "ensembl", 
-#'     gene_name = "gene_name", 
+#'     gene_ensembl = "ensembl",
+#'     gene_name = "gene_name",
 #'     suffix = "wrapper"
 #' )
+#'
+#' ## Explore the results from registration_wrapper()
+#' class(example_modeling_results)
+#' length(example_modeling_results)
+#' names(example_modeling_results)
+#' lapply(example_modeling_results, head)
 registration_wrapper <-
     function(sce,
     var_registration,
@@ -69,7 +75,8 @@ registration_wrapper <-
 
         ## Pseudobulk
         sce_pseudo <-
-            registration_pseudobulk(sce,
+            registration_pseudobulk(
+                sce,
                 var_registration = var_registration,
                 var_sample_id = var_sample_id,
                 min_ncells = min_ncells,
@@ -81,11 +88,14 @@ registration_wrapper <-
 
         block_cor <-
             registration_block_cor(sce_pseudo, registration_model = registration_mod)
-        
+
         ## test if registration var has two groups
         registration_var_k2 <- length(grep("^registration_variable", colnames(registration_mod))) == 2
         if (registration_var_k2) {
-          warning("You need 'var_registration' to have at least 3 different values to compute an F-statistic, returning Enrichment statistics only", call. = FALSE)
+            warning(
+                "You need 'var_registration' to have at least 3 unique values to compute an F-statistic and thus ANOVA modeling results cannot be computed.",
+                call. = FALSE
+            )
         }
 
         results_enrichment <-
@@ -96,40 +106,36 @@ registration_wrapper <-
                 gene_ensembl = gene_ensembl,
                 gene_name = gene_name
             )
-
-        ## with more than 2 groups run ANOVA and pairwise data
-        if(!registration_var_k2){
-          results_pairwise <-
+
+        results_pairwise <-
             registration_stats_pairwise(
-              sce_pseudo,
-              registration_model = registration_mod,
-              block_cor = block_cor,
-              gene_ensembl = gene_ensembl,
-              gene_name = gene_name
-            )
-          results_anova <-
-            registration_stats_anova(
-              sce_pseudo,
-              block_cor = block_cor,
-              covars = covars,
-              gene_ensembl = gene_ensembl,
-              gene_name = gene_name,
-              suffix = suffix
+                sce_pseudo,
+                registration_model = registration_mod,
+                block_cor = block_cor,
+                gene_ensembl = gene_ensembl,
+                gene_name = gene_name
             )
-
-          modeling_results <- list(
-            "anova" = results_anova,
-            "enrichment" = results_enrichment,
-            "pairwise" = results_pairwise
-          )
+
+        ## with more than 2 groups run ANOVA model
+        if (!registration_var_k2) {
+            results_anova <-
+                registration_stats_anova(
+                    sce_pseudo,
+                    block_cor = block_cor,
+                    covars = covars,
+                    gene_ensembl = gene_ensembl,
+                    gene_name = gene_name,
+                    suffix = suffix
+                )
         } else {
-          modeling_results <- list(
-            "anova" = NULL,
-            "enrichment" = results_enrichment,
-            "pairwise" = NULL
-          )
+            results_anova <- NULL
         }
-
 
+        ## Bundle results together
+        modeling_results <- list(
+            "anova" = NULL,
+            "enrichment" = results_enrichment,
+            "pairwise" = results_pairwise
+        )
         return(modeling_results)
     }
diff --git a/man/registration_wrapper.Rd b/man/registration_wrapper.Rd
diff --git a/tests/testthat/test-registration_wrapper.R b/tests/testthat/test-registration_wrapper.R
@@ -20,16 +20,17 @@ rowData(sce)$ensembl <- paste0("ENSG", seq_len(nrow(sce)))
 rowData(sce)$gene_name <- paste0("gene", seq_len(nrow(sce)))
 
 
-test_that("warning for k=2 variable",
-          example_modeling_results <- expect_warning(
-            registration_wrapper(
-              sce,
-              var_registration ="Treatment",
-              var_sample_id ="sample_id",
-              covars = c("age"),
-              gene_ensembl = "ensembl",
-              gene_name = "gene_name",
-              suffix = "wrapper"
-            )
-          )
+test_that(
+    "warning for k=2 variable",
+    example_modeling_results <- expect_warning(
+        registration_wrapper(
+            sce,
+            var_registration = "Treatment",
+            var_sample_id = "sample_id",
+            covars = c("age"),
+            gene_ensembl = "ensembl",
+            gene_name = "gene_name",
+            suffix = "wrapper"
+        )
+    )
 )