What are these dots in this boxplot?

July 27, 2023

I created a boxplot for a data set and did not use the geom_jitter function. Still there are dots inside the plot. Are those statistical values or why are they appearing?

I attached the code I use below.

pacman::p_load(tidyverse, readxl, janitor, emmeans, multcomp, magrittr,
               parameters, effectsize, multcompView, see, performance,
               conflicted, ggpubr, rstatix)
conflict_prefer("select", "dplyr")
conflict_prefer("filter", "dplyr")
conflict_prefer("summarise", "dplyr")
conflict_prefer("extract", "magrittr")

cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7") ## Color blind friendly palette
##--------------------------------------------------------------------------------------------------------------------------
## Funktion um Excel Datei mit mehreren Sheets zu öffnen und eines davon auszuwählen
library(readxl)    
read_excel_allsheets <- function(filename) {
  sheets <- readxl::excel_sheets(filename)
  x <- lapply(sheets, function(x) readxl::read_excel(filename, sheet = x))
  return(x)
}

big_tbl <- read_excel_allsheets ("Mesocosms_R.xlsx")
big_tbl

phyto_plankton_tbl<- big_tbl[[14]]
##--------------------------------------------------------------------------------------------------------------------------
## Data transformation
phyto_plankton_tbl %>% 
  mutate(
  block = as.factor(block),
  trt = factor(trt, labels = c("-P&-F", "+P/-F", "+P/+F", "-P/+F")))

phyto_plankton_tbl <- phyto_plankton_tbl %>% 
  gather(key = "time", value = "PelaChl", t0, t1, t2, t3, t4, t5) %>%  ## Ändert Tabelle aus width format into long format
  convert_as_factor(trt, time)
print(phyto_plankton_tbl, n = 40)
##--------------------------------------------------------------------------------------------------------------------------
## Visualization

pelaChl_bxp <- ggplot(data = phyto_plankton_tbl, aes(x= time, y = PelaChl, fill = trt)) +
  geom_boxplot() + 
  ylim(0, 50) +
  scale_fill_manual(values=cbPalette) + ## Adds color blind firendly palette
  ##  geom_jitter() +
  theme_bw()

>Solution :

From the documentation:

The boxplot compactly displays the distribution of a continuous variable. It visualises five summary statistics (the median, two hinges and two whiskers), and all "outlying" points individually.

The individual points you are seeing are outliers.