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Moss_CompileData.R
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################################################################################
### Peatland mosses: read taxa (ASV), add metadata and more
### Authors: Rachel Korn
### [email protected] University of Fribourg 20219 to 2023
################################################################################
library("phyloseq")
rm(list = ls())
gc()
source("Moss_readMetadataAndASV.R")
################################################################################
### Read ASV
asvDir <- "../smp_results"
### Prokaryotes
prok.l <- readTaxa(primer = "16S")
prok.l
list2env(prok.l, globalenv())
prok.a <- moss.a
# rm(moss, moss.a, moss.s, moss.r, prok.l)
### Eukaryotes
euk.l <- readTaxa(primer = "18S")
euk.l
list2env(euk.l, globalenv())
euk.a <- moss.a
rm(moss.a, euk.l)
## Save
# saveRDS(prok.a, "rds/Moss_prok.a.RDS")
# saveRDS(euk.a, "rds/Moss_euk.a.RDS")
### Merge both
## Renumber taxa
taxa_names(prok.a) <- paste0("ASV", seq(ntaxa(prok.a)))
taxa_names(prok.a)
taxa_names(euk.a) <- paste0("ASV", seq(ntaxa(prok.a) + 1,
ntaxa(prok.a) + ntaxa(euk.a)))
taxa_names(euk.a)
moss <- merge_phyloseq(prok.a, euk.a)
moss
### Save
# saveRDS(moss, "rds/Moss_moss.RDS")
### Export taxa table
taxa <- as.data.frame(tax_table(moss)@.Data)
otus <- as.data.frame(t(otu_table(moss)@.Data))
taxa_otus <- merge(taxa,
otus,
by = 0)
names(taxa_otus)[1] <- "ASV"
taxa_otus[, -c(1:7)] <- round(taxa_otus[, -c(1:7)],
digits = 7)
taxa_otus <- taxa_otus[do.call(order, taxa_otus[, c(2:7)]), ]
# write.table(taxa_otus, "Korn_et_al_Taxa-table.csv", row.names = FALSE)