Added easy16s visualization

easy16s-visu.R

@@ -0,0 +1,23 @@
+if (!requireNamespace("easy16S", quietly = TRUE)) {
+    # install.packages("remotes")
+    remotes::install_gitlab(
+        repo = "migale/easy16S@main",
+        host = "forgemia.inra.fr"
+    )
+}
+
+library(easy16S)
+library(MicroBioMap)
+library(phyloseq)
+library(mia)
+
+cpd <- getCompendium()
+cpd_phyloseq <- convertToPhyloseq(x = cpd)
+sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
+rm(cpd)
+gc()
+sample_data(cpd_phyloseq)
+cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
+rm(cpd_phyloseq)
+gc()
+easy16S::run_app(physeq = cpd_phyloseq_europe)