inst/doc/biomformat.R

In biomformat: An interface package for the BIOM file format

## ----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))