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# Discussion Figure 2 - Pressure audiograms for Elasmobranchs | |
setwd("H:/1. Shark Project/9. Data analysis/Behavioral Audiogram Analysis") | |
#getwd() | |
library(ggplot2) | |
library(ggpubr) | |
library(magrittr) | |
d <- read.table("Elasmo_audiogramms.txt",header=T,na.strings=c("NA","NaN",""),sep="\t") | |
#d <- d[d$study == 'CN' | d$study == 'ambient', ] | |
# First prepare a aggregated dataframe for average, upper boundary (average + 1SD) and lower boundary (average - 1SD) | |
# grouping by frequency and study. | |
d.agg <- aggregate(threshold ~ frequency + species, data = d, FUN = mean) | |
d.agg$upper <- aggregate(threshold ~ frequency + species, data = d, FUN = function(x) {mean(x) + sd(x)})$threshold | |
d.agg$lower <- aggregate(threshold ~ frequency + species, data = d, FUN = function(x) {mean(x) - sd(x)})$threshold | |
d.agg$N <- aggregate(threshold ~ frequency + species, data = d, FUN = length)$threshold | |
ggplot(d.agg, aes(frequency, threshold, color = species)) + | |
geom_line(aes(group = species, linetype = species)) + # add line | |
geom_point(aes(shape = species, color = species, fill = species)) + # add average (d.agg$frequency) point | |
geom_errorbar(aes(ymax = upper, ymin = lower)) + # add error bar (d.agg$lower and d.agg$upper) | |
# redefine three linetypes; google "R plot lty" to know the details | |
scale_linetype_manual(values = c(1,1,1,1,2,1,1,1)) + | |
# redefine three color | |
scale_color_manual(values = c("grey46", "darkorchid1", "steelblue2", "red","red", "black", "black", "green")) + | |
# redefine three shape and fill | |
scale_shape_manual(values = c(21,21,21,23,23,22, 22, 21, 21)) + # see ?pch | |
scale_fill_manual(values = c("grey46", "darkorchid1", "steelblue2", "red","white", "black", "white", "green")) + # "white" make orange point empty | |
# reforage y axis | |
scale_y_continuous( | |
name = "Sound Pressure Level (dB re 1uPa)", # y label | |
breaks = seq(90, 200, 5), # tick definition | |
limits = c(90, 180) # set limits | |
) + | |
# reforage x axis | |
scale_x_continuous( | |
trans = "log", | |
name = "Frequency [Hz]", # x label | |
breaks = c(seq(1,9,1), seq(10,90,10), seq(100,900,100),seq(1000,9000,1000)), # tick definition | |
labels = c(1,rep("", 8), 10,rep("", 8), 100,rep("", 8), 1000, rep("", 8)), | |
limits = c(9, 1500) # limits | |
) + | |
theme_pubr(base_size = 10, border = T, legend = "right") + # this theme from ggpubr package; highly recommanded | |
theme(legend.text = element_text(size = 10)) # make texts in legend 10 pt to adapt other texts | |
#scale_x_log10(breaks = trans_breaks("log10", function(x) 10^x), | |
#labels = trans_format("log10", math_format(10^.x))) + |
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