cosmetic changes in app_server

R/app_server.R

 #' @import shiny
-#' @importFrom DT DT
+#' @importFrom DT renderDT
 #' @importFrom phyloseq tax_table
+#' @importFrom phyloseq.extended write_phyloseq
 app_server <- function(input, output, session) {
   # Load package data in the session (for testing purpose)
   # data("physeq", package = "affiliationExplorer")
@@ -20,7 +21,6 @@ app_server <- function(input, output, session) {
     affi   <- all$affi  
     # Ambiguous ASVs and their affiliation
     ambiguous_otu <- unique(affi$OTU) ## this probably needs to be reactive
-    ambiguous_otu_affi <- phyloseq::tax_table(physeq)[ambiguous_otu, ] %>% as("matrix")
     # Add ASV Select Input
     insertUI(
       selector = "#tmp",

dev/02_dev.R

@@ -15,7 +15,7 @@ golem::add_module( name = "Main" ) # Name of the module
 usethis::use_pipe()
 
 usethis::use_package("shinydashboard")
-#usethis::use_package("shinycssloaders")
+usethis::use_package("shinycssloaders")
 #usethis::use_package("ReporteRs")
 usethis::use_package( "phyloseq" ) # To call each time you need a new package
 usethis::use_package( "biomformat" )