# #——包 ----------------------------------------------------------------- 图书馆(“biomformat”);packageVersion(“biomformat ") ## ---- read-biom-examples ------------------------------------------------------- min_dense_file =系统。文件(“extdata”、“min_dense_otu_table。Biom "， package = "biomformat") min_sparse_file =系统。文件(“extdata”、“min_sparse_otu_table。Biom "， package = "biomformat") rich_dense_file = system。文件(“extdata”、“rich_dense_otu_table。Biom "， package = "biomformat") rich_sparse_file = system。文件(“extdata”、“rich_sparse_otu_table。Biom "， package = "biomformat") min_dense_file =系统。文件(“extdata”、“min_dense_otu_table。Biom "， package = "biomformat")文件(“extdata”、“rich_dense_char。Biom "， package = "biomformat")文件(“extdata”、“rich_sparse_char。biom”,包= " 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 x1 # #——accessor-examples-table (rich_sparse_char) -------------------------------------------------- biom_data (x1) biom_data (x2) # #——matrix-coercion ---------------------------------------------------------- (biom_data (x2),“矩阵 ") ## ---- observ-meta -------------------------------------------------------------- observation_metadata (x1) observation_metadata (x2) observation_metadata (x3) observation_metadata (x4)(1:2, 1:3)类(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))