In brouwern/sparrowtelomeres: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(echo = TRUE, warning = F, error = F, message = F)

Example plot: beeswarm plot

# Prep stuff
## libraries
library(readxl)
library(ggpubr)
library(cowplot)
library(dplyr)
library(here)
library(plotrix)



file. <- "Meillere_et_al_2015_telomere_data.xlsx"

#load data
dat.full <- readxl::read_xlsx(here::here(file.), sheet = "orig")

dat.full$cort[is.na(dat.full$cort)] <-NA
# clean up data
dat.full$cort <- as.numeric(dat.full$cort)
dat.full$Group <- with(dat.full,
                       paste(treatment,sex))

dat.full$Group <- gsub("control","Control",dat.full$Group)
dat.full$Group <- gsub("disturbed","Noise exposure",dat.full$Group)

dat.full$Group <- gsub(" F","\nFemales",dat.full$Group)
dat.full$Group <- gsub(" M","\nMales",dat.full$Group)
dat.full$cort.log <- log(dat.full$cort)
dat.full$telomere.length.log <- log(dat.full$telomere.length)


names(dat.full) <- gsub("treatment",
                        "Treatment",
                        names(dat.full))

names(dat.full) <- gsub("sex",
                        "Sex",
                        names(dat.full))

dat.focal.cols <- dat.full[,c("Treatment","Sex","telomere.length","cort")]
dat.foc.cols.rnd <- dat.focal.cols
dat.foc.cols.rnd$telomere.length <- dat.foc.cols.rnd$telomere.length %>% round(1)
dat.foc.cols.rnd <- dat.foc.cols.rnd  %>% arrange(Treatment,telomere.length)

dat.foc.cols.rnd %>% 
  group_by(Treatment) %>% 
  summarise(sample.size = n(),
            min.telomere = min(telomere.length),
            max.telomore = max(telomere.length))

# Beeswarm plot
fx.up <- function(x) {mean(x)+1.96*std.error(x)}
fx.dwn <- function(x) {mean(x)-1.96*std.error(x)}
beeswarm. <- ggplot(dat.full,
        aes(y = telomere.length,
                   x = Treatment,
            fill = Treatment))+
   labs(title = "Beeswarm plot: raw data w/ means & error bars       ") +
    xlab("Predictor: Experimental group\n")+
          ylab("Response: Telomere length\n")+
  geom_dotplot(binaxis = "y",
               stackdir = "center",
               dotsize = 1.46) +
  stat_summary(fun.y = mean, 
               fun.ymin = mean, 
               fun.ymax = mean,
               geom = "crossbar", 
               width = 0.2,
               size = 0.45) + 
  stat_summary(fun.y = fx.up, 
               fun.ymin = fx.up, 
               fun.ymax = fx.up,
               geom = "crossbar", 
               width = 0.1,
               size = 0.35)+ 
  stat_summary(fun.y = fx.dwn, 
               fun.ymin = fx.dwn, 
               fun.ymax = fx.dwn,
               geom = "crossbar", 
               width = 0.1,
               size = 0.35) +
stat_summary(fun.y = mean, 
               fun.ymin = fx.dwn, 
               fun.ymax = fx.up,
               geom = "linerange", 
               width = 0.1,
               size = 0.35)

beeswarm.