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)