diff --git a/demo/demo.RData b/demo/demo.RData index 39d647f60f0418633155e26eff9c7fd29bcd1d62..950b79ed96c2747ca04c97e28a48af224ed1417b 100644 Binary files a/demo/demo.RData and b/demo/demo.RData differ diff --git a/demo/make-demo.R b/demo/make-demo.R index d546fb071b5beca64154dce34b26ba6598f609f5..c5c6da86ecc0272d36152c1fcfc77e29a7b9ddf8 100644 --- a/demo/make-demo.R +++ b/demo/make-demo.R @@ -1,57 +1,58 @@ -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") +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") +save(food, file = "demo.RData")