From 2b2d57e1b4f8661355865929ad987c012c13e235 Mon Sep 17 00:00:00 2001
From: Andreas Busjahn <abusjahn@healthtwist.de>
Date: Tue, 28 Nov 2023 10:33:41 +0100
Subject: [PATCH] label_outliers uses rownames/numbers if no labelvar
 detect_outliers returns now a list with values and positions

---
 R/plots.R              | 46 +++++++++++++++++++++++++-----------------
 man/detect_outliers.Rd |  5 ++++-
 man/label_outliers.Rd  |  4 ++--
 3 files changed, 34 insertions(+), 21 deletions(-)

diff --git a/R/plots.R b/R/plots.R
index 0fbbc8d..880488e 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -227,7 +227,7 @@ ggcormat <- function(cor_mat, p_mat = NULL,
 #' @param plotbase ggplot object to add labels to.
 # ' @param xvar x variable for grouping.
 # ' @param yvar y variable with possible outliers.
-#' @param labelvar variable to use as label.
+#' @param labelvar variable to use as label. If NULL, rownames or rownumbers are used.
 #' @param coef coefficient for boxplot.stats, defaults to 1.5.
 #' @param nudge_x nudge in x direction, defaults to 0.
 #' @param nudge_y nudge in y direction, defaults to 0.
@@ -241,40 +241,46 @@ ggcormat <- function(cor_mat, p_mat = NULL,
 # ' @examples
 # todo: group by facet variables
 #' @export
-label_outliers <- function(plotbase, labelvar, #xvar, #yvar,
+label_outliers <- function(plotbase, labelvar=NULL, #xvar, #yvar,
                            coef=1.5, nudge_x=0, nudge_y=0,
                            color="darkred", size=3, hjust=0,
                            face="bold") {
   if(!requireNamespace("ggrepel", quietly = TRUE)) {
     stop("ggrepel package is required")
   }
+  plotdata <- plotbase$data
+  if(is.null(labelvar)) {
+    labelvar <- "Position"
+    plotdata <- mutate(plotdata, Position = row.names(plotdata))
+  }
+  
   plotlist <- ggplot_build(plotbase)
   xvar <- plotbase$mapping[["x"]] |> as_label()
-    # plotlist[["plot"]][["layers"]][[1]][["computed_mapping"]][1] |> 
-    # as.character() |>
-    # str_remove("~")
+  # plotlist[["plot"]][["layers"]][[1]][["computed_mapping"]][1] |> 
+  # as.character() |>
+  # str_remove("~")
   yvar <- plotbase$mapping[["y"]] |> as_label()
-    #plotbase$layers[[1]]$computed_mapping[2] |> 
-    # plotlist[["plot"]][["layers"]][[1]][["computed_mapping"]][2] |> 
-    # as.character() |> 
-    # str_replace_all(
-    #   c('^.+\\"(.+)\\".*'="\\1",
-    #     "~"=""))
+  #plotbase$layers[[1]]$computed_mapping[2] |> 
+  # plotlist[["plot"]][["layers"]][[1]][["computed_mapping"]][2] |> 
+  # as.character() |> 
+  # str_replace_all(
+  #   c('^.+\\"(.+)\\".*'="\\1",
+  #     "~"=""))
   # groupvars <- xvar
   # if(!is.null(plotlist$layout$facet$params$row)){
-    facet_rows <- names(plotlist$layout$facet$params$row)
-    # groupvars <- c(groupvars,facet_rows)
+  facet_rows <- names(plotlist$layout$facet$params$row)
+  # groupvars <- c(groupvars,facet_rows)
   # }
   # if(!is.null(plotlist$layout$facet$params$col)){
-    facet_cols <- names(plotlist$layout$facet$params$col)
+  facet_cols <- names(plotlist$layout$facet$params$col)
   facet_wraps <- names(plotlist$layout$facet$params$facets)
   groupvars <- c(xvar,facet_rows,facet_cols,facet_wraps)
   outpositions <- 
     plotbase$data |> 
     group_by(across(all_of(groupvars))) |> 
     reframe(across(all_of(yvar),
-                   ~detect_outliers(.x, coef=coef))) |> 
-    left_join(plotbase$data)
+                   ~detect_outliers(.x, coef=coef)$outliers)) |> 
+    left_join(plotdata)
   plotbase + 
     ggrepel::geom_text_repel(data=outpositions,
                              aes(label=!!sym(labelvar)),
@@ -297,14 +303,18 @@ label_outliers <- function(plotbase, labelvar, #xvar, #yvar,
 #' @param x numeric vector.
 #' @param coef coefficient for boxplot.stats, defaults to 1.5. 
 #'
-#' @return A numeric vector with outliers.
+#' @return A list with elements positions and outliers as numeric vectors.
 #' 
+#' @examples
+#' detect_outliers(rnorm(100))
 #' @export
 detect_outliers <- function(x, coef=1.5) {
   qnt <- quantile(x, probs=c(.25, .75), na.rm = TRUE)
   iqr <- diff(qnt)
   upper <- qnt[2] + coef * iqr
   lower <- qnt[1] - coef * iqr
-  out <- x[x > upper | x < lower]
+  o_pos <- which(x > upper | x < lower)
+  out <- list("positions"=o_pos,
+              "outliers"=x[o_pos])
   return(out)
 }
diff --git a/man/detect_outliers.Rd b/man/detect_outliers.Rd
index d22370e..e421d7d 100644
--- a/man/detect_outliers.Rd
+++ b/man/detect_outliers.Rd
@@ -12,10 +12,13 @@ detect_outliers(x, coef = 1.5)
 \item{coef}{coefficient for boxplot.stats, defaults to 1.5.}
 }
 \value{
-A numeric vector with outliers.
+A list with elements positions and outliers as numeric vectors.
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 
 \code{detect_outliers} computes IQR and finds outliers. It gives the same results as \code{geom_boxplot} and thus differs slightly from \code{boxplot.stats}.
 }
+\examples{
+detect_outliers(rnorm(100))
+}
diff --git a/man/label_outliers.Rd b/man/label_outliers.Rd
index 62b36ae..46ea2b3 100644
--- a/man/label_outliers.Rd
+++ b/man/label_outliers.Rd
@@ -6,7 +6,7 @@
 \usage{
 label_outliers(
   plotbase,
-  labelvar,
+  labelvar = NULL,
   coef = 1.5,
   nudge_x = 0,
   nudge_y = 0,
@@ -19,7 +19,7 @@ label_outliers(
 \arguments{
 \item{plotbase}{ggplot object to add labels to.}
 
-\item{labelvar}{variable to use as label.}
+\item{labelvar}{variable to use as label. If NULL, rownames or rownumbers are used.}
 
 \item{coef}{coefficient for boxplot.stats, defaults to 1.5.}