make-demo.R

library(phyloseq)

data("GlobalPatterns")

food <-
  import_biom(
    BIOMfilename = "chaillou.biom",
    treefilename = "chaillou.nwk",
    parseFunction = parse_taxonomy_greengenes
  )
sample_data(food) <-
  read.table("chaillou.tsv",
             header = TRUE,
             row.names = 1,
             sep = "\t")

kinetic <-
  import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk")
sample_data(kinetic) <-
  read.table("mach.tsv",
             header = TRUE,
             row.names = 1,
             sep = "\t")
colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA

ravel <-
  import_biom(BIOMfilename = "ravel.biom")
sample_data(ravel) <-
  read.table("ravel.tsv",
             header = TRUE,
             row.names = 1,
             sep = "\t")
colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA

soil <-
  import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree")
sample_data(soil) <-
  read.table("morton.csv",
             header = TRUE,
             row.names = 1,
             sep = "\t")
colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA

biorare <-
  import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk")
sample_data(biorare) <-
  read.table("biorare.tsv", header = TRUE, row.names = 1)
colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA

# cellulose <- import_biom(BIOMfilename = "cellulose.biom")
# sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1)

save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData")