require(dplyr)
require(ggplot2)
require(tidyr)
require(reshape2)
require(lemon)
require(plotly)
require(data.table)
require(geobr)
require(terra)
require(openxlsx)
require(ggpubr)
require(ggpubr)
library("gpairs")
library(tidyverse)
library(GGally)


estacoes = read.xlsx('Data/stations.xlsx', detectDates = T)

a = filter(estacoes, as.numeric(chla_ugL) < 1000) %>%
      select(c('state', "chla_ugL",  'phycocianin_ugL','tss_mgL','tso_mgL', 'tsi_mgL', 'secchi_m',
               'dtc_mgL', 'doc_mgL','dic_mgL', 'turbidity_NTU', 'acdom440'))

a$chla_ugL =  (as.numeric(a$chla_ugL))
a$phycocianin_ugL =  (as.numeric(a$phycocianin_ugL))

a$tss_mgL =   (as.numeric(a$tss_mgL))
a$tsi_mgL =   (as.numeric(a$tsi_mgL))
a$tso_mgL =   (as.numeric(a$tso_mgL))

a$acdom440 =  (as.numeric(a$acdom440))
a$secchi_m = (as.numeric(a$secchi_m))
a$dtc_mgL = (as.numeric(a$dtc_mgL))
a$doc_mgL = (as.numeric(a$doc_mgL))
a$dic_mgL = (as.numeric(a$dic_mgL))
a$turbidity_NTU = (as.numeric(a$turbidity_NTU))

names(a)



names(a) = c("estado_sigla", "Chl-a", 'PC', 
             "TSS", "TSO", "TSI", "Zsd",'DTC', "DOC", 'DIC', "Turbidity" ,"aCDOM(440)")


a$`Chl-a` = log(a$`Chl-a`)
a$TSS = log(a$TSS)
a$Zsd = log(a$Zsd)
a$`aCDOM(440)` = log(a$`aCDOM(440)`)

plt = a %>% mutate(estado_sigla = as.factor(estado_sigla)) %>%
  ggpairs(columns = c("Chl-a", 
                      "TSS", "Zsd","aCDOM(440)"), 
          aes(color = estado_sigla),
          upper = list(continuous = wrap('cor', size = 13)),
          lower = list(combo = wrap("facethist", bins = 30)),
          diag = list(continuous = wrap("barDiag", alpha = 0.8))) +
  #scale_x_log10(labels = label_number()) +
  #scale_y_log10(labels = label_number()) +
  theme_bw() + 
  theme(panel.grid.major = element_line(colour = "#d3d3d3"),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank(),
        panel.spacing = unit(2, "lines"),
        text=element_text(family = "Tahoma", size = 25),
        axis.title = element_text( size = 40),
        axis.text.x = element_text(colour="black", size = 40),
        axis.text.y = element_text(colour="black", size = 40),
        axis.line = element_line(size=2, colour = "black"),
        strip.text = element_text(size=40)) 


ggsave(plot = plt, filename = 'Outputs/Figures/Figure_08_log.jpeg', 
       width = 30, height = 25, dpi = 200, units = 'in')


plotly::ggplotly(plt)



# rafa


cor(log(a[,-1]), na.rm = T)


cor(log(a[,-1]), use = "pairwise.complete.obs")