polarolouis/human-microbiome-compendium
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Louis 2025-11-14 10:52:29 +01:00
parent 3570b94f49
commit 354ee4d528
3 changed files with 24 additions and 3 deletions
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data/hmc-phyloseq.Rds Normal file
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7
load-europe.R
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@ -2,13 +2,14 @@ library(MicroBioMap)
library(phyloseq) library(phyloseq)
library(mia) library(mia)
if (!file.exists("data/hmc-phyloseq-europe.Rds")) { if (!(file.exists("data/hmc-phyloseq-europe.Rds") || file.exists("data/hmc-phyloseq.Rds"))) {
cpd <- getCompendium() cpd <- getCompendium()
cpd_phyloseq <- convertToPhyloseq(x = cpd) cpd_phyloseq <- convertToPhyloseq(x = cpd)
sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe") # sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
rm(cpd) rm(cpd)
gc() gc()
sample_data(cpd_phyloseq) # sample_data(cpd_phyloseq)
saveRDS(cpd_phyloseq, "data/hmc-phyloseq.Rds")
cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name)) cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
rm(cpd_phyloseq) rm(cpd_phyloseq)
gc() gc()

20
load-full.R Normal file
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@ -0,0 +1,20 @@
library(MicroBioMap)
library(phyloseq)
library(mia)
if (!(file.exists("data/hmc-phyloseq-europe.Rds") || file.exists("data/hmc-phyloseq.Rds"))) {
cpd <- getCompendium()
cpd_phyloseq <- convertToPhyloseq(x = cpd)
# sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
rm(cpd)
gc()
# sample_data(cpd_phyloseq)
saveRDS(cpd_phyloseq, "data/hmc-phyloseq.Rds")
cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
rm(cpd_phyloseq)
gc()
saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds")
} else {
cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds")
cpd_phyloseq <- readRDS("data/hmc-phyloseq.Rds")
}