Now, ref.group option is also considereded in two samples mean compar…

…isons #118

NEWS.md

@@ -13,6 +13,8 @@
 
 ## Bug fixes
 
+- The option `ref.group` was only considered when the grouping variable contains more than two levels. In that case, each level is compared against the specified reference group. Now, `ref.group` option is also considereded in two samples mean comparisons ([@OwenDonohoe, #118](https://github.com/kassambara/ggpubr/issues/118)
+
 - Now, `ggqqplot()` reacts to the argument `conf.int.level` ([@vsluydts, #123](https://github.com/kassambara/ggpubr/issues/123)
 - Added error bar color is now inherited from the main plot ([@JesseRop, #109](https://github.com/kassambara/ggpubr/issues/109)
 

R/compare_means.R

@@ -156,6 +156,9 @@ compare_means <- function(formula, data, method = "wilcox.test",
     if(is.factor(group.vals)) group.levs <- levels(group.vals)
     else group.levs <- unique(group.vals)
 
+    if(ref.group %in% group.levs){
+      data[, group] <- stats::relevel(group.vals, ref.group)
+    }
 
     if(ref.group == ".all."){
       data <- data %>%

R/stat_compare_means.R

@@ -199,7 +199,7 @@ StatCompareMeans<- ggproto("StatCompareMeans", Stat,
                     #::::::::::::::::::::::::::::::::::::::::::::::::::
                     method.args <- method.args %>%
                       .add_item(data = data, method = method,
-                                paired = paired, ref.group = ref.group,
+                                paired = paired, ref.group = as.character(ref.group),
                                 symnum.args = symnum.args)
 
                     if(.is.multiple.grouping.vars){
@@ -212,6 +212,7 @@ StatCompareMeans<- ggproto("StatCompareMeans", Stat,
                         .add_item(formula = y ~ x)
                       .test <- do.call(compare_means, method.args)
                     }
+                    print(.test)
 
                     pvaltxt <- ifelse(.test$p < 2.2e-16, "p < 2.2e-16",
                                       paste("p =", signif(.test$p, 2)))