fix: factor variables auto converted to characters

R/oncoplot.R

@@ -125,8 +125,14 @@ ggoncoplot <- function(.data,
   }
   if(!is.null(col_mutation_type)){
     assertions::assert_string(col_mutation_type)
-    # Assert mutation type columne sensible
+    # Assert mutation type is a valid column name
     assertions::assert_names_include(.data, col_mutation_type)
+
+    # If column type is a factor, convert to character
+    if(is.factor(.data[[col_mutation_type]])) .data[[col_mutation_type]] <- as.character(.data[[col_mutation_type]])
+
+    # Assert column type = character
+    #assertions::assert_character(.data[[col_mutation_type]])
     assertions::assert_no_missing(.data[[col_mutation_type]], arg_name = paste0("Mutation Type Column: ", col_mutation_type))
     assertions::assert_excludes(.data[[col_mutation_type]], illegal = "", msg = "{.strong Mutation Type} column cannot contain zero-length strings")
   }
@@ -153,10 +159,14 @@ ggoncoplot <- function(.data,
   }
 
   #Assert sample column sensible
+  if(is.factor(.data[[col_samples]])) .data[[col_samples]] <- as.character(.data[[col_samples]])
+  assertions::assert_character(.data[[col_samples]])
   assertions::assert_no_missing(.data[[col_samples]])
   assertions::assert_excludes(.data[[col_samples]], illegal = "", msg = "{.strong Sample} column cannot contain zero-length strings") # Asserts no empty string
 
   #Assert gene column sensible
+  if(is.factor(.data[[col_genes]])) .data[[col_genes]] <- as.character(.data[[col_genes]])
+  assertions::assert_character(.data[[col_genes]])
   assertions::assert_no_missing(.data[[col_genes]])
   assertions::assert_excludes(.data[[col_genes]], illegal = "", msg = "{.strong Gene} column cannot contain zero-length strings") # Asserts no empty string
 

tests/testthat/test-ggoncoplot_simulated_data.R

@@ -163,14 +163,37 @@ test_that("ggoncoplot works with pathway mapping", {
 
   #NFE2L2 & EMPTY should both be in final plot
 
-  gg <- suppressMessages(ggoncoplot(
+  expect_error(
+    gg <- suppressMessages(ggoncoplot(
     df_mutations,
     col_genes = "Genes",
     col_samples = "Samples",
     col_mutation_type = "VariantType", interactive = TRUE, topn = Inf,
     pathway = df_pathway
-  ))
+  )), NA
+  )
 })
 
 
+test_that("ggoncoplot works with factor-type columns", {
+
+  # Create a version of the data
+  df_mutations_factor <- df_mutations
+  df_mutations_factor[["Genes"]] <- as.factor(df_mutations[["Genes"]])
+  df_mutations_factor[["Samples"]] <- as.factor(df_mutations[["Samples"]])
+  df_mutations_factor[["VariantType"]] <- as.factor(df_mutations[["VariantType"]])
+
+  expect_error(
+    suppressMessages(ggoncoplot(
+      df_mutations_factor,
+      col_genes = "Genes",
+      col_samples = "Samples",
+      col_mutation_type = "VariantType"
+    )),
+    NA
+  )
+})
+
+
+
 

vignettes/quick_start.Rmd

@@ -364,14 +364,12 @@ gbm_df |>
 ggoncoplot outputs can be combined with other packages. Simply set interactive = FALSE so ggoncoplot returns a ggplot object instead of a ggiraph. Do the same for express. Then you can con
 
 ```{r}
-
-
 ## Create a Glioblastoma Oncoplot
 ggoncoplot <- gbm_df |>
   ggoncoplot(
     col_genes = 'Hugo_Symbol',
     col_samples = 'Tumor_Sample_Barcode',
-    col_mutation_type = 'Variant_Classification',
+    col_mutation_type = 'Variant_Classification', 
     interactive = FALSE
   )