v0.2.0, added more positions for letters, etc

Update NEWS.md

Author: ethanbass

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggtukey
 Title: Compact Letter Displays for 'ggplot2'
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: 
     person("Ethan", "Bass", , "ethanbass@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6175-6739"))
@@ -10,7 +10,7 @@ Description: Provides a simple interface to visualize paired comparisons in 'ggp
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Requires: R >= 4.1.0
 Imports: 
     dplyr,

NAMESPACE

@@ -13,11 +13,13 @@ import(multcompView)
 import(rlang)
 importFrom(dplyr,left_join)
 importFrom(magrittr,"%>%")
+importFrom(rlang,as_name)
 importFrom(stats,IQR)
 importFrom(stats,TukeyHSD)
 importFrom(stats,aov)
 importFrom(stats,as.formula)
 importFrom(stats,median)
 importFrom(stats,quantile)
 importFrom(stats,reorder)
+importFrom(stats,sd)
 importFrom(tidyr,drop_na)

NEWS.md

@@ -1,3 +1,10 @@
+# ggtukey 0.2.0
+
+* Added additional options to `where` parameter for placement of letters.
+* Allowed numeric arguments to `type` argument in `geom_tukey`.
+* Added citation file.
+* Changed `vjust` default to `-0.2`.
+
 # ggtukey 0.1.0
 
 * Added a `NEWS.md` file to track changes to the package.

R/boxplot_letters.R

@@ -19,8 +19,11 @@
 #' test (with an interaction term between \code{x} and \code{group}). Defaults
 #' to \code{two-way}. This argument only applies if the Tukey test is selected,
 #' since there is no two-way Kruskal-Wallis test.
-#' @param where Where to place the letters. Either above the box (\code{box}),
-#' above the upper whisker (\code{whisker}).
+#' @param where Where to put the letters. Either above the box (\code{box}) or
+#' upper whisker (\code{whisker}) of a boxplot; at the \code{mean} or
+#' \code{median}; or at the top of the error bars calculated from the standard
+#' error (\code{se}), standard deviation \code{sd}, or 95% confidence intervals
+#' returned by \code{\link[Hmisc]{smean.cl.normal}}, or \code{\link[Hmisc]{smean.cl.boot}}.
 #' @param raw Whether to plot raw data and (if so), how. The current options are
 #' \code{none}, \code{\link[ggplot2]{geom_point}}, \code{\link[ggplot2]{geom_dotplot}}, or
 #' \code{\link[ggplot2]{geom_jitter}}.
@@ -41,7 +44,8 @@
 #' @importFrom stats TukeyHSD aov as.formula median quantile reorder
 #' @import rlang
 #' @author Ethan Bass
-#' @note Adapted from https://www.mathiasecology.com/code/add-tukeys-significant-letters-to-ggplots
+#' @note Adapted from a helpful \href{https://www.mathiasecology.com/code/add-tukeys-significant-letters-to-ggplots}{blog post}
+#' by \href{https://github.com/justinmathias}{Justin Mathias}.
 #' @return Returns the specified plot as a \code{ggplot} object.
 #' @examples
 #' set.seed(1)
@@ -53,14 +57,17 @@
 #' @export
 
 boxplot_letters <- function(data, x, y, fill, group, test = c("tukey", "kruskalmc"),
-                            type=c("two-way", "one-way"), where = c("box","whisker"),
+                            type=c("two-way", "one-way"),
+                            where = c("box","whisker", "mean", "median",
+                                      "se", "sd", "cl_normal", "cl_boot"),
                             raw = c('none', 'points', 'dots', 'jitter'),
-                            pt_col = "slategray", ..., hjust=0, vjust=0,
+                            pt_col = "slategray", ..., hjust = 0, vjust = -0.2,
                             lab_size = 4, na.rm = TRUE, threshold = 0.05){
   test <- match.arg(test, c("tukey", "kruskalmc"))
   raw <- match.arg(raw, c('none', 'points', 'dots', 'jitter'))
   type <- match.arg(type, c("two-way","one-way"))
-  where <- match.arg(where, c("box","whisker"))
+  where <- match.arg(where, c("box","whisker", "mean", "median",
+                              "se", "sd", "cl_normal", "cl_boot"))
   x.s <- deparse(substitute(x))
   y.s <- deparse(substitute(y))
 

R/geom_tukey.R

@@ -5,11 +5,13 @@
 #' @param type If a grouping variable is provided, determines whether to run
 #' separate tests for each facet (\code{one-way}) or one (\code{two-way}) test with
 #' an interaction term between \code{x} and \code{group}. Defaults to \code{two-way}.
-#' @param where Where to put the letters. Either above the box (\code{box}),
-#' above the upper whisker (\code{whisker}), or at the \code{mean} or
-#' \code{median}.
-#' @param hjust Horizontal adjustment of the label. Argument to \code{\link[ggplot2]{geom_text}}.
-#' @param vjust Vertical adjustment of the label. Argument to \code{\link[ggplot2]{geom_text}}.
+#' @param where Where to put the letters. Either above the box (\code{box}) or
+#' upper whisker (\code{whisker}) of a boxplot; at the \code{mean} or
+#' \code{median}; or at the top of the error bars calculated from the standard
+#' error (\code{se}), standard deviation \code{sd}, or 95% confidence intervals
+#' returned by \code{\link[Hmisc]{smean.cl.normal}}, or \code{\link[Hmisc]{smean.cl.boot}}.
+#' @param hjust Horizontal adjustment of the label. (Argument to \code{\link[ggplot2]{geom_text}}).
+#' @param vjust Vertical adjustment of the label. (Argument to \code{\link[ggplot2]{geom_text}}).
 #' @param size Label size. Argument to \code{\link[ggplot2]{geom_text}}.
 #' @param na.rm Logical. Whether to remove observations with NAs for the provided
 #' factors (i.e. \code{x} and \code{group}) before plotting. Defaults to TRUE.
@@ -26,10 +28,11 @@
 #' * Graves S, Piepho H, Dorai-Raj LSwhfS (2019). multcompView: Visualizations
 #' of Paired Comparisons. R package version 0.1-8. \url{https://CRAN.R-project.org/package=multcompView}
 #'
-#' @note Thank you to Hiroaki Yutani (\url{https://yutani.rbind.io/post/2017-11-07-ggplot-add/})
-#' and Simon P Couch (\url{https://www.simonpcouch.com/blog/ggplot-pipe-plus/})
-#' for a couple of very helpful blog posts describing the \code{\link[ggplot2]{ggplot_add}}
-#' syntax.
+#' @note Thank you to \href{https://github.com/yutannihilation}{Hiroaki Yutani}
+#' and \href{https://github.com/simonpcouch}{Simon P. Couch} for a couple of
+#' very helpful blog posts (\href{https://yutani.rbind.io/post/2017-11-07-ggplot-add/}{1},
+#' \href{https://www.simonpcouch.com/blog/ggplot-pipe-plus/}{2}) describing the
+#' \code{\link[ggplot2]{ggplot_add}} syntax.
 #' @examples
 #' library(ggplot2)
 #' set.seed(1)
@@ -42,13 +45,18 @@
 
 geom_tukey <- function(test = c("tukey","kruskalmc"), threshold = 0.05,
                        type=c("two-way", "one-way"),
-                       where = c("box","whisker", "mean", "median"),
-                       hjust=0, vjust=0, size = 4, na.rm = TRUE){
+                       where = c("box","whisker", "mean", "median", "se", "sd",
+                                 "cl_normal", "cl_boot"),
+                       hjust = 0, vjust = -0.2, size = 4, na.rm = TRUE){
   # store inputs in classed output that can
   # be passed to a `ggplot_add` method
   test <- match.arg(test, c("tukey", "kruskalmc"))
+  if (is.numeric(type)){
+    type <- switch(type, "1"="one-way", "2"="two-way")
+  }
   type <- match.arg(type, c("two-way", "one-way"))
-  where <- match.arg(where,  c("box","whisker", "mean", "median"))
+  where <- match.arg(where,  c("box", "whisker", "mean", "median",
+                               "se", "sd","cl_normal","cl_boot"))
   if (test == "kruskalmc"){
     type <- "one-way"
   }
@@ -71,8 +79,8 @@ geom_tukey <- function(test = c("tukey","kruskalmc"), threshold = 0.05,
 #' @noRd
 geom_tukey_ <- function(p, test = c("tukey","kruskalmc"), threshold = 0.05,
                         type=c("two-way", "one-way"),
-                        where = c("box","whisker", "mean","median"),
-                        hjust=0, vjust=0, size = 4, na.rm = TRUE) {
+                        where = c("box","whisker", "mean","median", "se", "sd","cl_normal","cl_boot"),
+                        hjust = 0, vjust = 0, size = 4, na.rm = TRUE) {
   data <- p$data
   if (na.rm){
     data <- drop_na(data, !!p$mapping$x, !!p$facet$params$facets[[1]])
@@ -85,7 +93,7 @@ geom_tukey_ <- function(p, test = c("tukey","kruskalmc"), threshold = 0.05,
       data <- get_tukey_letters(data = data,
                                 x = c(p$mapping$x, p$facet$params$facets[[1]]),
                                 y= p$mapping$y, test = test,
-                                where = where,type = type,
+                                where = where, type = type,
                                 threshold = threshold)
     } else if (type == "one-way"){
       data <- get_tukey_letters(data = data,

R/utils.R

@@ -2,23 +2,27 @@
 #' Do Tukey Test and calculate letter placement
 #' @importFrom stats TukeyHSD aov as.formula median quantile reorder
 #' @importFrom dplyr left_join
+#' @importFrom rlang as_name
 #' @param data A data.frame in long format
 #' @param x Independent variable or vector of variables to plot on x axis
 #' @param y Response variable to plot on y axis
 #' @param test Which test to run for pairwise comparisons. Either \code{tukey}
 #' (\code{\link[stats]{TukeyHSD}}) or \code{\link[pgirmess]{kruskalmc}}. Defaults
 #' to \code{tukey}.
-#' @param where Where to put the letters. Either above the box (\code{box}) or
-#' above the upper whisker (\code{whisker}).
+#' @param where Where to put the letters. Either above the box (\code{box}),
+#' above the upper whisker (\code{whisker}), or at the \code{mean} or
+#' \code{median}.
 #' @param threshold Statistical threshold for significance. Defaults to 0.05.
 #' @noRd
 
-get_tukey_letters <- function(data, x, y, group=NULL, test = c("tukey", "kruskalmc"),
+get_tukey_letters <- function(data, x, y, group = NULL, test = c("tukey", "kruskalmc"),
                               type = c("two-way", "one-way"),
-                              where=c("box", "whisker", "mean", "median"),
+                              where = c("box", "whisker", "mean",
+                                        "median", "se", "sd", "cl_normal","cl_boot"),
                               threshold = 0.05){
   test <- match.arg(test, c("tukey", "kruskalmc"))
-  where <- match.arg(where, c("box", "whisker", "mean","median"))
+  where <- match.arg(where, c("box", "whisker", "mean","median", "se", "sd",
+                              "cl_normal", "cl_boot"))
   type <- match.arg(type, c("two-way", "one-way"))
   if (inherits(x, "quosure") & is.null(group)){
     letters.df <- place_tukey_letters(data, as_name(x), as_name(y), test = test,
@@ -69,7 +73,11 @@ place_tukey_letters <- function(data, x, y, test = c("tukey", "kruskalmc"),
                           "box" = get_quantile,
                           "whisker" = get_whisker,
                           "mean" = mean,
-                          "median" = median)
+                          "median" = median,
+                          "se" = get_sem,
+                          "sd" = get_sd,
+                          "cl_normal" = get_cl_normal,
+                          "cl_boot" = get_cl_boot)
   placement <- data %>% # Create a dataframe to assign the letter position.
     group_by(.data[[xlab]]) %>%
     summarise("Placement.Value" = placement_fnc(.data[[y]]))
@@ -80,6 +88,28 @@ place_tukey_letters <- function(data, x, y, test = c("tukey", "kruskalmc"),
   letters.df
 }
 
+#' @importFrom stats sd
+#' @noRd
+get_sem <- function(x){
+  mean(x) + sd(x)/sqrt(length(x))
+}
+
+#' @importFrom stats sd
+#' @noRd
+get_sd <- function(x){
+  mean(x) + sd(x)
+}
+
+#' @noRd
+get_cl_normal <- function(x){
+  Hmisc::smean.cl.normal(x)[[3]]
+}
+
+#' @noRd
+get_cl_boot <- function(x){
+  Hmisc::smean.cl.boot(x)[[3]]
+}
+
 #' Check whether color specifications exists.
 #'
 #' @export

README.md

@@ -54,7 +54,7 @@ For more examples and details on different options for customization, please con
 
 You can cite `ggtukey` as follows:
 
-Bass, E. (2022). ggtukey: Compact Letter Displays for 'ggplot2' (v0.1.0). (https://ethanbass.github.io/ggtukey/). 
+Bass, E. (2022). ggtukey: Compact Letter Displays for 'ggplot2' (v0.2.0). (https://ethanbass.github.io/ggtukey/). 
 
 # Further Reading
 

inst/CITATION

@@ -0,0 +1,14 @@
+citHeader("To cite ggtukey in publications, please use:")
+
+citEntry(
+  entry    = "manual",
+  title    = "ggtukey: Compact Letter Displays for 'ggplot2'",
+  author   = "Ethan Bass",
+  year     = "2023",
+  note     = "version 0.2.0",
+  url      = "https://ethanbass.github.io/ggtukey/",
+  doi      = "",
+  textVersion = paste("Bass, E. (2023).",
+        "ggtukey: Compact Letter Displays for 'ggplot2' (version 0.2.0)."
+        )
+  )