fix for #30

NEWS.md

@@ -4,6 +4,8 @@
 
 ## Minor changes
 
+- Significance levels can be now customized and passed to `stat_compare_means()` ([@jaison75, #45](https://github.com/kassambara/ggpubr/issues/30)).
+
 ## Bug fixes
 
 - In `ggscatterhist()` the x variable was plotted two times, on both the plot x & y margins, instead of having, as expected, a) the x variable on the main plot x margin and 2) the y variable on the main plot y margin. This has been now fixed. 
@@ -14,7 +16,7 @@
 
 - New function `ggballoonplot()` added to visualize a contingency table.
 
-- `ggdotchart()` can be now used to plot multiple groups with `position = position_dodge()` [@ManuelSpinola, #45](https://github.com/kassambara/ggpubr/issues/45).
+- `ggdotchart()` can be now used to plot multiple groups with `position = position_dodge()` ([@ManuelSpinola, #45](https://github.com/kassambara/ggpubr/issues/45)).
 
 - New function `ggscatterhist()` to create a scatter plot with marginal histograms, density plots and box plots.
 

R/stat_compare_means.R

@@ -123,7 +123,18 @@ stat_compare_means <- function(mapping = NULL, data = NULL,
     if(.is_p.signif_in_mapping(mapping) | (label %in% "p.signif"))
       {
       map_signif_level <- c("****"=0.0001, "***"=0.001, "**"=0.01,  "*"=0.05, "ns"=1)
-      if(hide.ns) names(map_signif_level)[5] <- " "
+      if(hide.ns) map_signif_level <- .hide_ns(map_signif_level)
+    }
+
+    if(!.is_empty(symnum.args)){
+
+      symnum.args.isok <- length(symnum.args$cutpoints == length(symnum.args$symbols))
+      if(!symnum.args.isok)
+        stop("Incorrect format detected in symnum.args. ",
+             "Check the documentation.")
+      map_signif_level <- symnum.args$cutpoints[-1] # the first element is 0 (the minimum p-value)
+      names(map_signif_level) <- symnum.args$symbols
+      if(hide.ns) map_signif_level <- .hide_ns(map_signif_level)
     }
 
     step_increase <- ifelse(is.null(label.y), 0.12, 0)
@@ -302,6 +313,15 @@ StatCompareMeans<- ggproto("StatCompareMeans", Stat,
   mapping
 }
 
+# Hide NS in map_signif_level
+.hide_ns <- function(x){
+  n <- names(x)
+  ns.pos <- which(n == "ns" | n == "NS")
+  if(!.is_empty(ns.pos)) n[ns.pos] = " "
+  names(x) <- n
+  x
+}
+