## ----packages----------------------------------------------------------------- library("biomformat"); packageVersion("biomformat") ## ----read-biom-examples------------------------------------------------------- min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat") min_sparse_file = system.file("extdata", "min_sparse_otu_table.biom", package = "biomformat") rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom", package = "biomformat") rich_sparse_file = system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat") min_dense_file = system.file("extdata", "min_dense_otu_table.biom", package = "biomformat") rich_dense_char = system.file("extdata", "rich_dense_char.biom", package = "biomformat") rich_sparse_char = system.file("extdata", "rich_sparse_char.biom", package = "biomformat") x1 = read_biom(min_dense_file) x2 = read_biom(min_sparse_file) x3 = read_biom(rich_dense_file) x4 = read_biom(rich_sparse_file) x5 = read_biom(rich_dense_char) x6 = read_biom(rich_sparse_char) x1 ## ----accessor-examples-table-------------------------------------------------- biom_data(x1) biom_data(x2) ## ----matrix-coercion---------------------------------------------------------- as(biom_data(x2), "matrix") ## ----observ-meta-------------------------------------------------------------- observation_metadata(x1) observation_metadata(x2) observation_metadata(x3) observation_metadata(x4)[1:2, 1:3] class(observation_metadata(x4)) ## ----plot-examples------------------------------------------------------------ sample_metadata(x1) sample_metadata(x2) sample_metadata(x3) sample_metadata(x4)[1:2, 1:3] class(sample_metadata(x4)) ## ----plot--------------------------------------------------------------------- plot(biom_data(x4)) boxplot(as(biom_data(x4), "vector")) heatmap(as(biom_data(x4), "matrix")) ## ----write-biom-examples------------------------------------------------------ outfile = tempfile() write_biom(x4, outfile) y = read_biom(outfile) identical(x4, y) ## ----compare-files-diff, eval=FALSE------------------------------------------- # # On Unix OSes # system(paste0("diff ", rich_sparse_file, outfile)) # # On windows # system(paste0("FC ", rich_sparse_file, outfile))