Commit f5aec7b4 authored by Midoux Cedric's avatar Midoux Cedric Committed by Guillaume Perréal
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demo : chaillou only

parent 7a514800
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library(phyloseq) library(phyloseq)
data("GlobalPatterns") data("GlobalPatterns")
food <- food <-
import_biom( import_biom(
BIOMfilename = "chaillou.biom", BIOMfilename = "chaillou.biom",
treefilename = "chaillou.nwk", treefilename = "chaillou.nwk",
parseFunction = parse_taxonomy_greengenes parseFunction = parse_taxonomy_greengenes
) )
sample_data(food) <- sample_data(food) <-
read.table("chaillou.tsv", read.table("chaillou.tsv",
header = TRUE, header = TRUE,
row.names = 1, row.names = 1,
sep = "\t") sep = "\t")
kinetic <- kinetic <-
import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk") import_biom(BIOMfilename = "mach.biom", treefilename = "mach.nwk")
sample_data(kinetic) <- sample_data(kinetic) <-
read.table("mach.tsv", read.table("mach.tsv",
header = TRUE, header = TRUE,
row.names = 1, row.names = 1,
sep = "\t") sep = "\t")
colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus") colnames(tax_table(kinetic)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")
tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA tax_table(kinetic)[grep("unknown ", tax_table(kinetic))] <- NA
ravel <- ravel <-
import_biom(BIOMfilename = "ravel.biom") import_biom(BIOMfilename = "ravel.biom")
sample_data(ravel) <- sample_data(ravel) <-
read.table("ravel.tsv", read.table("ravel.tsv",
header = TRUE, header = TRUE,
row.names = 1, row.names = 1,
sep = "\t") sep = "\t")
colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") colnames(tax_table(ravel)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA tax_table(ravel)[grep("unknown ", tax_table(ravel))] <- NA
soil <- soil <-
import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree") import_biom(BIOMfilename = "morton.biom", treefilename = "morton.tree")
sample_data(soil) <- sample_data(soil) <-
read.table("morton.csv", read.table("morton.csv",
header = TRUE, header = TRUE,
row.names = 1, row.names = 1,
sep = "\t") sep = "\t")
colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") colnames(tax_table(soil)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA tax_table(soil)[grep("unknown ", tax_table(soil))] <- NA
biorare <- biorare <-
import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk") import_biom(BIOMfilename = "biorare.biom", treefilename = "biorare.nwk")
sample_data(biorare) <- sample_data(biorare) <-
read.table("biorare.tsv", header = TRUE, row.names = 1) read.table("biorare.tsv", header = TRUE, row.names = 1)
colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") colnames(tax_table(biorare)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA tax_table(biorare)[grep("unknown ", tax_table(biorare))] <- NA
# cellulose <- import_biom(BIOMfilename = "cellulose.biom") # cellulose <- import_biom(BIOMfilename = "cellulose.biom")
# sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1) # sample_data(cellulose) <- read.table("cellulose.tsv", header = TRUE, row.names = 1)
save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData") # save(GlobalPatterns, food, kinetic, soil, ravel, biorare, file = "demo.RData")
save(food, file = "demo.RData")
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