Circle_Plot_PCBs

#Circos plot of PCBs >LOQ, categorized by number of chlorines 

library(tidyverse)
install.packages("ggtext")
library(ggtext)
install.packages("patchwork")
library(patchwork)
library(ggplot2)

#code from https://r-graph-gallery.com/297-circular-barplot-with-groups.html
# Set a number of 'empty bar' to add at the end of each group
data <- read.xlsx("NADA.xlsx", sheet = "percent_LOQ") 

data <- read.xlsx("test.xlsx")

# Set a number of 'empty bar'
empty_bar <- 30

# Add lines to the initial dataset
to_add <- matrix(NA, empty_bar, ncol(data))
colnames(to_add) <- colnames(data)
data <- rbind(data, to_add)
data$id <- seq(1, nrow(data))


# prepare a data frame for base lines
base_data <- data %>% 
  group_by(group) %>% 
  #summarize(start=min(id), end=max(id) - empty_bar) %>% 
  summarize(start=min(id), end=max(id)) %>%
  rowwise() %>% 
  mutate(title=mean(c(start, end)))

# prepare a data frame for grid (scales)
grid_data <- base_data
grid_data$end <- grid_data$end[ c( nrow(grid_data), 1:nrow(grid_data)-1)] + 1
grid_data$start <- grid_data$start - 1
grid_data <- grid_data[-1,]



# Make the plot
p <- ggplot(data, aes(x=as.factor(id), y=value, fill=group)) +       # Note that id is a factor. If x is numeric, there is some space between the first bar
  
  geom_bar(aes(x=as.factor(id), y=value, fill=group), stat="identity", alpha=0.5) +
  # Add a val=50/10 lines. I do it at the beginning to make sure barplots are OVER it.
  geom_segment(data=grid_data, aes(x = end, y = 50, xend = start, yend = 50), colour = "azure4", alpha=0.8, size=0.3 , inherit.aes = FALSE ) +
  geom_segment(data=grid_data, aes(x = end, y = 10, xend = start, yend = 10), colour = "azure4", alpha=0.8, size=0.3 , inherit.aes = FALSE ) +
  
  # Add text showing the value of each 50/10 lines
  annotate("text", x = rep(max(data$id),2), y = c(10, 50), label = c("10%", "50%") , color="azure4", size=1.8 , angle=0, fontface="bold", hjust=1) +
  
  geom_bar(aes(x=as.factor(id), y=value, fill= group), stat="identity", alpha=0.5) +
  scale_fill_brewer(palette="RdBu") +
  ylim(-50,120) +
  theme_minimal() +
  theme(
    legend.position = "none",
    axis.text = element_blank(),
    axis.title = element_blank(),
    panel.grid = element_blank(),
    plot.margin = unit(rep(-1,4), "cm") 
  ) +
  coord_polar() + 
  
  
  # Add base line information
  geom_segment(data=base_data, aes(x = start, y = -3, xend = end, yend = -3), alpha=0.8, size=0.35 , inherit.aes = FALSE, colour = "black")  +
  geom_text(data=base_data, aes(x = title, y = -17, label=group), hjust=0.5, colour = "black", alpha=0.8, size=1.8, angle= 0, fontface="plain", inherit.aes = FALSE)
p