diff --git a/data/hmc-phyloseq.Rds b/data/hmc-phyloseq.Rds new file mode 100644 index 0000000..426b626 Binary files /dev/null and b/data/hmc-phyloseq.Rds differ diff --git a/load-europe.R b/load-europe.R index 6fa2254..4cb5db9 100644 --- a/load-europe.R +++ b/load-europe.R @@ -2,13 +2,14 @@ library(MicroBioMap) library(phyloseq) 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_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) 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)) rm(cpd_phyloseq) gc() diff --git a/load-full.R b/load-full.R new file mode 100644 index 0000000..c379a29 --- /dev/null +++ b/load-full.R @@ -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") +}