R/visualize_database.R

In Eliot-RUIZ/eDNAevaluation: Metabarcodes Evaluation

## Requirement: 'webr'

# Info: Function designed to get a quick overview of the differences between the databases

visualize_database = function(data1, data2, data3, data4, data5, plot = NULL, print = T){
  
  names_of_dataframes = c(deparse(substitute(data1)), deparse(substitute(data2)), deparse(substitute(data3)), 
                          deparse(substitute(data4)), deparse(substitute(data5)))
  
  number_sequences = c(nrow(data1), nrow(data2), nrow(data3), nrow(data4), nrow(data5))
  
  number_species = c(length(unique(data1$SPECIES)), length(unique(data2$SPECIES)), length(unique(data3$SPECIES)), 
                     length(unique(data4$SPECIES)), length(unique(data5$SPECIES)))
  
  number_genus = c(length(unique(data1$GENUS)), length(unique(data2$GENUS)), length(unique(data3$GENUS)), 
                   length(unique(data4$GENUS)), length(unique(data5$GENUS)))
  
  number_families = c(length(unique(data1$FAMILY)), length(unique(data2$FAMILY)), length(unique(data3$FAMILY)), 
                      length(unique(data4$FAMILY)), length(unique(data5$FAMILY)))
  
  number_orders = c(length(unique(data1$ORDER)), length(unique(data2$ORDER)), length(unique(data3$ORDER)), 
                    length(unique(data4$ORDER)), length(unique(data5$ORDER)))
  
  table_numbers = tibble(data.frame(DATABASES = names_of_dataframes,
                                    SEQUENCES = number_sequences, SPECIES = number_species, GENUS = number_genus, 
                                    FAMILIES = number_families, ORDERS = number_orders))
  
  if(!is.null(plot)) {
    
    if(plot == 1 || plot == 2 || plot == 3 || plot == 4) {
      
      PieDonut(get(names_of_dataframes[plot], .GlobalEnv), aes(ORDER, FAMILY), explodePie = T, explodeDonut = F, 
               ratioByGroup = T, showPieName = T, showDonutName = T, pieLabelSize = 4, showRatioThreshold = 0.8,
               labelpositionThreshold = 0.0001, labelposition = 1000, maxx = 1.3, 
               title = paste0(names_of_dataframes[plot], ": Families & Orders"))
      
    }
    
  }
  
  if(print) print(table_numbers)
  
}