Commit 1305af2c authored by Olivier Rue's avatar Olivier Rue
Browse files

toto

parent 2b0792da
Pipeline #48184 passed with stage
in 25 seconds
...@@ -126,6 +126,7 @@ if (!file.exists("REAL_MEAT/ITS1.rds")) { ...@@ -126,6 +126,7 @@ if (!file.exists("REAL_MEAT/ITS1.rds")) {
metadata <- read.table("REAL_MEAT/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE) metadata <- read.table("REAL_MEAT/metadata.tsv", row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
sample_data(physeq_its1) <- metadata sample_data(physeq_its1) <- metadata
sample_data(physeq_its1)$Marker <- "ITS1" sample_data(physeq_its1)$Marker <- "ITS1"
sample_data(physeq_its1)$Type <- "Raw"
sample_data(physeq_its1)$Reads <- raw_data %>% filter(Ecosystem == "MEAT") %>% filter(Marker == "ITS1") %>% pull(Reads) sample_data(physeq_its1)$Reads <- raw_data %>% filter(Ecosystem == "MEAT") %>% filter(Marker == "ITS1") %>% pull(Reads)
sample_names(physeq_its1) <- glue::glue(paste("{sample_names(physeq_its1)}","ITS1", sep="_")) sample_names(physeq_its1) <- glue::glue(paste("{sample_names(physeq_its1)}","ITS1", sep="_"))
saveRDS(physeq_its1,"REAL_MEAT/ITS1.rds") saveRDS(physeq_its1,"REAL_MEAT/ITS1.rds")
...@@ -261,6 +262,11 @@ ggVennDiagram(x,label_alpha = 0) + ...@@ -261,6 +262,11 @@ ggVennDiagram(x,label_alpha = 0) +
```{r, eval=T} ```{r, eval=T}
physeq_its1_final <- curation_meat_its1(physeq_its1) physeq_its1_final <- curation_meat_its1(physeq_its1)
sample_data(physeq_its1_final)$Type <- "Curated"
sample_data(physeq_its1_final)$Reads <- sample_sums(physeq_its1_final)
sample_names(physeq_its1_final) <- glue::glue(paste("{sample_names(physeq_its1)}","CURATED", sep="_"))
saveRDS(physeq_its1_final,"REAL_MEAT/ITS1_final.rds") saveRDS(physeq_its1_final,"REAL_MEAT/ITS1_final.rds")
physeq_its2_final <- curation_meat_its2(physeq_its2) physeq_its2_final <- curation_meat_its2(physeq_its2)
......
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