# 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)
sessionInfo()
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
## 
## time zone: Europe/Oslo
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] viridis_0.6.5     viridisLite_0.4.2 lubridate_1.9.4   forcats_1.0.0    
##  [5] stringr_1.5.1     dplyr_1.1.4       purrr_1.0.2       readr_2.1.5      
##  [9] tidyr_1.3.1       tibble_3.2.1      tidyverse_2.0.0   ggplot2_3.5.1    
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.9        generics_0.1.3    stringi_1.8.4     lattice_0.22-6   
##  [5] hms_1.1.3         digest_0.6.37     magrittr_2.0.3    evaluate_1.0.1   
##  [9] grid_4.4.2        timechange_0.3.0  fastmap_1.2.0     jsonlite_1.8.9   
## [13] Matrix_1.7-1      gridExtra_2.3     mgcv_1.9-1        scales_1.3.0     
## [17] textshaping_0.4.1 jquerylib_0.1.4   cli_3.6.3         rlang_1.1.4      
## [21] munsell_0.5.1     splines_4.4.2     withr_3.0.2       cachem_1.1.0     
## [25] yaml_2.3.10       tools_4.4.2       tzdb_0.4.0        colorspace_2.1-1 
## [29] vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4   ragg_1.3.3       
## [33] pkgconfig_2.0.3   pillar_1.10.0     bslib_0.8.0       gtable_0.3.6     
## [37] glue_1.8.0        systemfonts_1.1.0 xfun_0.49         tidyselect_1.2.1 
## [41] rstudioapi_0.17.1 knitr_1.49        farver_2.1.2      htmltools_0.5.8.1
## [45] nlme_3.1-166      rmarkdown_2.29    labeling_0.4.3    compiler_4.4.2