From a6298fadcdc25c08a9e5ca50ca805153617dd8f2 Mon Sep 17 00:00:00 2001 From: Louis Date: Mon, 13 Oct 2025 10:25:50 +0200 Subject: [PATCH] Using new loading script in easy16s visu --- easy16s-visu.R | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/easy16s-visu.R b/easy16s-visu.R index 6e13187..db9d33c 100644 --- a/easy16s-visu.R +++ b/easy16s-visu.R @@ -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)