Plotting_NDVI_Shannon

# Labels

labels = c(bacteria = "Bacteria",
           fits1 =  "Fungi (ITS1)",
           fits2 = "Fungi (ITS2)",
           oomycetes = "Oomycetes",
           nematodes = "Nematodes")

signif.labs <- c("pval > 0.05", "pval <= 0.05")
names(signif.labs) <- c("p value > 0.05", "p value <= 0.05")

# Pivot table


all_taxa_data_long <- pivot_longer(all_taxa_data, 
                                        cols = c(ndvi, 
                                                 Shannon),
                                        names_to = "type", 
                                        values_to = "value")
# Add significance


all_taxa_data_temp <- all_taxa_data %>%
  add_column("pval") %>%
  mutate(pval = ifelse(Taxa == "nematodes" , 0.00496, NA)) %>%
  mutate(pval = ifelse(Taxa == "fits1",0.6, pval)) %>%
  mutate(pval = ifelse(Taxa == "fits2",0.6, pval)) %>%
  mutate(pval = ifelse(Taxa == "bacteria",0.6, pval)) %>%
  mutate(pval = ifelse(Taxa == "oomycetes",0.6, pval)) %>%
  mutate(signif = ifelse(pval <= 0.05, "pval <= 0.05", "pval > 0.05"))


all_taxa_data <- all_taxa_data_temp


# Scatter plot by group

theme_set(theme_bw())

ndvi_shannon_all <- ggplot(all_taxa_data,
                           aes(x = ndvi,
                               y = Shannon,
                               color = Taxa,
                               shape = Taxa)) +
  geom_point(alpha = 0.8, size = 3) +
  geom_smooth(method = "glm", formula = y~x, se = F,
                      method.args = list(family = gaussian(link = 'log')),
              aes(color = Taxa, linetype = signif)) +
  scale_shape_discrete(name = "Taxa", labels = labels,
                       breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes")) +
  scale_color_viridis(name = "Taxa",
                      labels = labels,
                      begin = 0,
                      end = 0.8,
                       breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes"),
                      discrete = TRUE) +
   scale_linetype_discrete(name= 'Significance',
                           guide = 'none') +
                     #labels = names(signif.labs)) +
  #scale_linetype_manual(name = "Taxa",
                        #breaks = c("bacteria", "fits1", "fits2", "nematodes", "oomycetes")) +
  theme(plot.title = element_text(hjust = 0.5 #,size = 20 
                                  ), 
        panel.grid.major = element_blank(), 
        panel.grid.minor = element_blank(),
        panel.background = element_blank(),
        strip.background = element_blank()) +
  
        #axis.text = element_text(size = 20),
        #text = element_text(size = 24)
    xlab("NDVI") + 
    ylab("Alpha diversity")
  

ndvi_shannon_all

save_plot(ndvi_shannon_all, plot_name = paste0("ndvi_shannon_all"),
          plot_width=13, plot_height=18)