From aa824b130bb8d5b988911c45004ecfc6b2a015d9 Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Sun, 17 Aug 2025 17:25:17 +0200
Subject: [PATCH] Added easy16s visualization

---
 easy16s-visu.R | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 easy16s-visu.R

diff --git a/easy16s-visu.R b/easy16s-visu.R
new file mode 100644
index 0000000..6e13187
--- /dev/null
+++ b/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)