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Using new loading script in easy16s visu

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Louis 2025-10-13 10:25:50 +02:00
parent 099a654a21
commit a6298fadcd
1 changed files with 6 additions and 12 deletions
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18
easy16s-visu.R
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@ -7,17 +7,11 @@ if (!requireNamespace("easy16S", quietly = TRUE)) {
}
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()
if (!file.exists("data/hmc-phyloseq-europe.Rds")) {
source("load-europe.R")
} else {
cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds")
}
easy16S::run_app(physeq = cpd_phyloseq_europe)