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Adding a boxplot with outliers function

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1 parent bd7dd5b commit 7646d1c7f6ddd43e203c55c131dd9ca71f32c6ef @talgalili committed Feb 17, 2012
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  1. +236 −0 boxplot.with.outlier.label.r
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+# some helpful threads
+# https://stat.ethz.ch/pipermail/r-help/2008-September/172641.html
+# http://tolstoy.newcastle.edu.au/R/e4/help/08/02/4875.html
+# http://tolstoy.newcastle.edu.au/R/e2/help/07/01/8598.html
+
+# http://www.r-statistics.com/wp-content/uploads/2011/01/boxplot-add-label-for-outliers.r.txt
+
+# last updated: 31.10.2011
+# This is instead of the 20.6.11 version...
+
+boxplot.with.outlier.label <- function(y, label_name, ..., spread_text = T, data, plot = T, range = 1.5, label.col = "blue", push_text_right = 1.3, # enlarge push_text_right in order to push the text labels further from their point
+segement_width_as_percent_of_label_dist = .45, # Change this if you want to have the line closer to the label (range should be between 0 to 1
+ jitter_if_duplicate = T, jitter_only_positive_duplicates = F)
+{
+ # notes - this functions doesn't work if there are any missing values in the data.
+ # You must pre-process the data to make sure it is "complete".
+
+
+ # change log:
+ # 19.04.2011 - added support to "names" and "at" parameters.
+
+
+ # jitter_if_duplicate - will jitter (Actually just add a bit of numbers) so to be able to decide on which location to plot the label when having identical variables...
+ require(plyr) # for is.formula and ddply
+
+ # a function to jitter data in case of ties in Y's
+ jitter.duplicate <- function(x, only_positive = F)
+ {
+ if(only_positive) {
+ ss <- x > 0
+ } else {
+ ss <- T
+ }
+ ss_dup <- duplicated(x[ss])
+ # ss <- ss & ss_dup
+ temp_length <- length(x[ss][ss_dup])
+ x[ss][ss_dup] <- x[ss][ss_dup] + seq(from = 0.00001, to = 0.00002, length.out = temp_length)
+ x
+ }
+ # jitter.duplicate(c(1:5))
+ # jitter.duplicate(c(1:5,5,2))
+ # duplicated(jitter.duplicate(c(1:5,5,2)))
+ # jitter.duplicate(c(0,0,1:5,5,2))
+ # duplicated(jitter.duplicate(c(0,0,1:5,5,2)))
+
+
+
+ # handle cases where
+ if(jitter_if_duplicate) {
+ # warning("duplicate jutter of values in y is ON")
+ if(!missing(data)) { #e.g: we DO have data
+ # if(exists("y") && is.formula(y)) { # F && NULL # F & NULL
+ y_name <- as.character(substitute(y)) # I could have also used as.list(match.call())
+ # credit to Uwe Ligges and Marc Schwartz for the help
+ # https://mail.google.com/mail/?shva=1#inbox/12dd7ca2f9bfbc39
+ if(length(y_name) > 1) { # then it is a formula (for example: "~", "y", "x"
+ model_frame_y <- model.frame(y, data = data)
+ temp_y <- model_frame_y[,1]
+ temp_y <- jitter.duplicate(temp_y, jitter_only_positive_duplicates) # notice that the default of the function is to work only with positive values...
+ # the_txt <- paste(names(model_frame_y)[1], "temp_y", sep = "<<-") # wrong...
+ the_txt <- paste("data['",names(model_frame_y)[1],"'] <- temp_y", sep = "")
+ eval(parse(text = the_txt)) # jutter out y var so to be able to handle identical values.
+ } else { # this isn't a formula
+ data[,y_name] <- jitter.duplicate(data[,y_name], jitter_only_positive_duplicates)
+ y <- data[,y_name] # this will make it possible for boxplot(y, data) to work later (since it is not supposed to work with data when it's not a formula, but now it does :))
+ }
+ } else { # there is no "data"
+ if(is.formula(y)) { # if(exists("y") && is.formula(y)) { # F && NULL # F & NULL
+ temp_y <- model.frame(y)[,1]
+ temp_y <- jitter.duplicate(temp_y, jitter_only_positive_duplicates) # notice that the default of the function is to work only with positive values...
+ temp_y_name <- names(model.frame(y))[1] # we must extract the "names" before introducing a new enbironment (or there will be an error)
+ environment(y) <- new.env()
+ assign(temp_y_name, temp_y, environment(y))
+ # Credit and thanks for doing this goes to Niels Richard Hansen (2 Jan 30, 2011)
+ # http://r.789695.n4.nabble.com/environment-question-changing-variables-from-a-formula-through-model-frame-td3246608.html
+ # warning("Your original variable (in the global environemnt) was just jittered.") # maybe I should add a user input before doing this....
+ # the_txt <- paste(names(model_frame_y)[1], "temp_y", sep = "<<-")
+ # eval(parse(text = the_txt)) # jutter out y var so to be able to handle identical values.
+ } else {
+ y <- jitter.duplicate(y, jitter_only_positive_duplicates)
+ }
+ }
+ }
+ # the_txt <- paste("print(",names(model_frame_y)[1], ")")
+ # eval(parse(text = the_txt)) # jutter out y var so to be able to handle identical values.
+ # print(ls())
+
+
+ # y should be a formula of the type: y~x, y~a*b
+ # or it could be simply y
+ if(missing(data)) {
+ boxdata <- boxplot(y, plot = plot,range = range ,...)
+ } else {
+ boxdata <- boxplot(y, plot = plot,data = data, range = range ,...)
+ }
+ if(length(boxdata$names) == 1 && boxdata$names =="") boxdata$names <- 1 # this is for cases of type: boxplot(y) (when there is no dependent group)
+ if(length(boxdata$out) == 0 ) {
+ warning("No outliers detected for this boxplot")
+ return(invisible())
+ }
+
+ if(!missing(data)) attach(data) # this might lead to problams I should check out for alternatives for using attach here...
+
+
+ # creating a data.frame with information from the boxplot output about the outliers (location and group)
+ boxdata_group_name <- factor(boxdata$group)
+ levels(boxdata_group_name) <- boxdata$names[as.numeric(levels(boxdata_group_name))] # the subseting is for cases where we have some sub groups with no outliers
+ if(!is.null(list(...)$at)) { # if the user chose to use the "at" parameter, then we would like the function to still function (added on 19.04.2011)
+ boxdata$group <- list(...)$at[boxdata$group]
+ }
+ boxdata_outlier_df <- data.frame(group = boxdata_group_name, y = boxdata$out, x = boxdata$group)
+
+
+ # Let's extract the x,y variables from the formula:
+ if(is.formula(y))
+ {
+ model_frame_y <- model.frame(y)
+ # old solution: (which caused problems if we used the names parameter when using a 2 way formula... (since the order of the names is different then the levels order we get from using factor)
+ # y <- model_frame_y[,1]
+ # x <- model_frame_y[,-1]
+
+ y <- model_frame_y[,1]
+ x <- model_frame_y[,-1]
+ if(!is.null(dim(x))) { # then x is a matrix/data.frame of the type x1*x2*..and so on - and we should merge all the variations...
+ x <- apply(x,1, paste, collapse = ".")
+ }
+ } else {
+ # if(missing(x)) x <- rep(1, length(y))
+ x <- rep(1, length(y)) # we do this in case y comes as a vector and without x
+ }
+
+ # and put all the variables (x, y, and outlier label name) into one data.frame
+ DATA <- data.frame(label_name, x ,y)
+
+ if(!is.null(list(...)$names)) { # if the user chose to use the names parameter, then we would like the function to still function (added on 19.04.2011)
+ DATA$x <- factor(DATA$x, levels = unique(DATA$x))
+ levels(DATA$x) = list(...)$names # enable us to handle when the user adds the "names" parameter # fixed on 19.04.11 # notice that DATA$x must be of the "correct" order (that's why I used split above
+ # warning("Careful, the use of the 'names' parameter is experimental. If you notice any errors please e-mail me at: tal.galili@gmail.com")
+ }
+
+ if(!missing(data)) detach(data) # we don't need to have "data" attached anymore.
+
+ # let's only keep the rows with our outliers
+ boxplot.outlier.data <- function(xx, y_name = "y")
+ {
+ y <- xx[,y_name]
+ boxplot_range <- range(boxplot.stats(y, coef = range )$stats)
+ ss <- (y < boxplot_range[1]) | (y > boxplot_range[2])
+ return(xx[ss,])
+ }
+ outlier_df <-ddply(DATA, .(x), boxplot.outlier.data)
+
+
+ # create propor x/y locations to handle over-laping dots...
+ if(spread_text) {
+ # credit: Greg Snow
+ require(TeachingDemos)
+ temp_x <- boxdata_outlier_df[,"x"]
+ temp_y1 <- boxdata_outlier_df[,"y"]
+ temp_y2 <- temp_y1
+ for(i in unique(temp_x))
+ {
+ tmp <- temp_x == i
+ temp_y2[ tmp ] <- spread.labs( temp_y2[ tmp ], 1.3*strheight('A'), maxiter=6000, stepsize = 0.05) #, min=0 )
+ }
+
+ }
+
+
+
+ # max(strwidth(c("asa", "a"))
+ # move_text_right <- max(strwidth(outlier_df[,"label_name"]))
+
+ # plotting the outlier labels :) (I wish there was a non-loop wise way for doing this)
+ for(i in seq_len(dim(boxdata_outlier_df)[1]))
+ {
+ # ss <- (outlier_df[,"x"] %in% boxdata_outlier_df[i,]$group) & (outlier_df[,"y"] %in% boxdata_outlier_df[i,]$y)
+
+ # if(jitter_if_duplicate) {
+ # ss <- (outlier_df[,"x"] %in% boxdata_outlier_df[i,]$group) & closest.number(outlier_df[,"y"] boxdata_outlier_df[i,]$y)
+ # } else {
+ ss <- (outlier_df[,"x"] %in% boxdata_outlier_df[i,]$group) & (outlier_df[,"y"] %in% boxdata_outlier_df[i,]$y)
+ # }
+
+ current_label <- outlier_df[ss,"label_name"]
+ temp_x <- boxdata_outlier_df[i,"x"]
+ temp_y <- boxdata_outlier_df[i,"y"]
+ # cbind(boxdata_outlier_df, temp_y2)
+ # outlier_df
+
+
+
+ if(spread_text) {
+ temp_y_new <- temp_y2[i] # not ss
+ move_text_right <- strwidth(current_label) * push_text_right
+ text( temp_x+move_text_right, temp_y_new, current_label, col = label.col)
+ # strwidth
+ segments( temp_x+(move_text_right/6), temp_y, temp_x+(move_text_right*segement_width_as_percent_of_label_dist), temp_y_new )
+ } else {
+ text(temp_x, temp_y, current_label, pos = 4, col = label.col)
+ }
+ }
+
+ # outputing some of the information we collected
+ invisible(list(boxdata = boxdata, boxdata_outlier_df = boxdata_outlier_df, outlier_df=outlier_df))
+}
+
+
+
+
+
+
+########################################
+### examples to see that it works
+
+# library(plyr)
+# library(TeachingDemos)
+# source("http://www.r-statistics.com/wp-content/uploads/2011/01/boxplot-with-outlier-label-r.txt") # Load the function
+# set.seed(210)
+# n <- 20
+# y <- rnorm(n)
+# x1 <- sample(letters[1:3], n,T)
+# lab_y <- sample(letters, n)
+# boxplot.with.outlier.label(y~x1, lab_y, push_text_right = 1.5, range = .3)
+# data.frame(y, x1, lab_y)
+
+# set.seed(10)
+# x2 <- sample(letters[1:3], n,T)
+# boxplot.with.outlier.label(y~x1*x2, lab_y, push_text_right = 1.5, range = .3)
+# data.frame(y, x1, x2, lab_y)
+
+
+# y1 <- y
+# y1[1] <- NA
+# boxplot.with.outlier.label(y1~x1, lab_y, push_text_right = 1.5, range = .3)
+

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