Calculate go enrichment improvement

NEWS.md

@@ -1,8 +1,13 @@
 # protti 0.9.1.9000
 
+## New features 
+
+* `calculate_go_enrichment()` received the argument `label_size` that allows the user to specifiy the size of the labels in the plot.
+
 ## Bug fixes
 
 * Fixed issue #193. This makes sure that information in retained columns can be propagated to newly created combinations, which were not present in the original data.
+* `calculate_go_enrichment()` can now correctly handle groups that are of type factor.
 
 ## Additional Changes
 

R/calculate_go_enrichment.R

@@ -78,6 +78,8 @@ go_enrichment <- function(...) {
 #' should be reversed in order. Default is `TRUE`.
 #' @param label a logical argument indicating whether labels should be added to the plot.
 #' Default is TRUE.
+#' @param label_size a numeric argument that specifies the text size of the labels with the unit "pt".
+#' The default is 7.
 #' @param enrichment_type a character argument that is either "all", "enriched" or "deenriched". This
 #' determines if the enrichment analysis should be performed in order to check for both enrichemnt and
 #' deenrichemnt or only one of the two. This affects the statistics performed and therefore also the displayed
@@ -223,6 +225,7 @@ calculate_go_enrichment <- function(data,
                                     heatmap_fill_colour = protti::mako_colours,
                                     heatmap_fill_colour_rev = TRUE,
                                     label = TRUE,
+                                    label_size = 7,
                                     enrichment_type = "all",
                                     replace_long_name = TRUE,
                                     label_move_frac = 0.2,
@@ -408,12 +411,14 @@ if you used the right organism ID.", prefix = "\n", initial = ""))
   }
 
   result_table <- cont_table %>%
+    dplyr::arrange({{ group }}) %>%
     { # group argument is missing
       if (group_missing) {
         dplyr::left_join(., fisher_test, by = "go_id")
       } else {
         # group argument is not missing
         dplyr::left_join(., fisher_test, by = c("go_id", rlang::as_name(enquo(group)))) %>%
+          dplyr::mutate({{ group }} := forcats::fct_inorder({{ group }})) %>%
           dplyr::group_by({{ group }})
       }
     } %>%
@@ -529,12 +534,16 @@ if you used the right organism ID.", prefix = "\n", initial = ""))
               ),
               y = .data$neg_log_sig - 0.1,
               hjust = .data$hjust
-            )
+            ),
+            size = label_size / .pt
           )
         }
       } +
       ggplot2::scale_fill_manual(values = c(Deenriched = barplot_fill_colour[1], Enriched = barplot_fill_colour[2])) +
-      ggplot2::scale_y_continuous(labels = scales::number_format(accuracy = 1)) +
+      ggplot2::scale_y_continuous(
+        labels = scales::number_format(accuracy = 1),
+        expand = expansion(mult = c(0, 0.05))
+      ) +
       ggplot2::coord_flip() +
       {
         if (!missing(group)) {
@@ -605,7 +614,11 @@ if you used the right organism ID.", prefix = "\n", initial = ""))
         if (group_missing) {
           dplyr::mutate(., grouping = "")
         } else {
-          dplyr::mutate(., grouping = forcats::fct_inorder({{ group }}))
+          if (!is(dplyr::pull(plot_input, {{ group }}), "factor")) { # if the column is already a factor do not reorder
+            dplyr::mutate(., grouping = forcats::fct_inorder({{ group }}))
+          } else {
+            dplyr::mutate(., grouping = {{ group }})
+          }
         }
       }
 
@@ -659,10 +672,13 @@ if you used the right organism ID.", prefix = "\n", initial = ""))
               NA
               )
             ),
-            colour = plot_input_heatmap$text_col
+            colour = plot_input_heatmap$text_col,
+            size = label_size / .pt
           )
         }
       } +
+      ggplot2::scale_x_discrete(expand = expansion(mult = c(0, 0))) +
+      ggplot2::scale_y_discrete(expand = expansion(mult = c(0, 0))) +
       ggplot2::scale_fill_gradientn(colours = colours) +
       ggplot2::labs(
         title = plot_title,