demo : chaillou only

demo/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")
+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")