Symbiobase

library(tidyverse)
library(lubridate)
library(DT)
library(RColorBrewer)


collections <- read.csv("https://raw.githubusercontent.com/symbiobase/symbioID/main/Symbiobase.csv")  |>
  dplyr::select(sample_id, collection_date, location, site, longitude, latitude, host_family, host_genus, host_species, sym_type_1) |>
  rename(symbiont=sym_type_1) |> 
  mutate(latitude=round(latitude,3), longitude=round(longitude,3), collection_date=ymd(collection_date)) |> 
  mutate(location = gsub("_", " ", location),
         site = gsub("_", " ", site),
         host_genus = gsub("_", " ", host_genus),
         host_species = gsub("_", " ", host_species)) |> 
  mutate(symbiont = ifelse(is.na(symbiont), "Upon request", symbiont)) |> 
  filter(!symbiont == "?") |> 
  # mutate(latitudinal_band = as.character(cut(latitude, breaks = seq(-34, -13, by = 1), include.lowest = TRUE))) %>%
  # mutate(latitudinal_band = gsub(",", " to ", latitudinal_band) %>%
  #                          gsub("\\]", ")", .) %>%
  #                          gsub("(-?\\d+)", "\\1°S", .)) %>%
  arrange(symbiont)



# Generate a color palette for host_species
unique_genera <- unique(collections$host_genus)
genera_colors <- colorRampPalette(brewer.pal(12, "Set3"))(length(unique_genera))
names(genera_colors) <- unique_genera

datatable(collections,  
          rownames = FALSE, 
          colnames = c('Sample ID' = 'sample_id', 'Collection date' = 'collection_date', 'Location' = 'location', 
                       "Site" = "site", 'Longitude' = "longitude", 'Latitude' = 'latitude', 
                       "Host family" = "host_family", "Host genus" = "host_genus", "Host species" = "host_species", 
                       "Symbiont"= "symbiont"),
          filter = 'top', 
          extensions = c('Buttons', 'RowGroup', 'Scroller', 'Select', 'SearchPanes'), 
          options = list(pageLength = 20, 
                         autoWidth = TRUE,
                         rowGroup = list(dataSrc = 7),
                         selection = 'none',
#                         dom = 'Bfrtip',
                         buttons = c('copy', 'csv', 'excel'),
                         deferRender = TRUE,
                         scrollY = 1000,
                         scroller = TRUE,
                         dom = 'Pfrtip', 
                        columnDefs = list(list(searchPanes = list(show = FALSE), targets = c(1,2,4,5,6)))
                         )
            ) %>%
  # formatStyle(
  #   c('Sample ID', 'Collection date', 'Location',  "Site", 'Longitude', 'Latitude', 
  #     "Host family", "Host genus", "Host species", "Latitudinal Band"),
  #   fontSize = '90%'
  # ) %>%
  formatStyle(
    columns=c('Sample ID', 'Collection date', 'Location',  "Site", 'Longitude', 'Latitude', 
      "Host family", "Host genus", "Host species", "Symbiont"),
   valueColumns='Host genus',
    backgroundColor = styleEqual(names(genera_colors), genera_colors),
   fontSize = '90%'
  ) %>%
  formatStyle(
    c('Host genus','Host species'),
    fontStyle = 'italic'
  )