library(ggplot2)
library(tidyverse)

f = read.table("/Users/HW/OneDrive_University_of_Edinburgh/OneDrive - University of Edinburgh/PhD_Research/Species_Identification_meta-analysis/05_Salix_RAD/05_down_sampling/Number_of_spps_mono_for_boxplot_m40.txt", check.names=FALSE, header=TRUE)
## boxplot
#boxplot(f)

d <- pivot_longer(f, cols = 1:length(colnames(f)), names_to = "Number_of_SNPs", values_to = "Number_of_species_discriminated")
Number_SNPs <- as.numeric(d$Number_of_SNPs)
Number_species_discriminated <- as.numeric(d$Number_of_species_discriminated)

ggplot(data = d) +
  geom_boxplot(aes(x = Number_SNPs, y = Number_species_discriminated, group = Number_SNPs)) +
  scale_y_continuous(minor_breaks = seq(0 , 50, 1), breaks = seq(0, 50, 2)) +
  geom_smooth(aes(x = Number_SNPs, y = Number_species_discriminated), size = 0.8, se=FALSE) +
  labs(title = "Numbers of species discriminated by Monophyly - Salix", x = "Number_SNPs", y = "Number_species_discriminated") +
  theme_light()