Nothing
# Example metadata for BIOM object
b_otu_ids <- c("denovo0", "denovo1", "denovo2", "denovo3", "denovo5")
b_sample_ids <- c("A.1", "A.2", "B.1", "B.2", "C.1")
b_taxonomy <- list(
"Bacteria",
"Bacteria",
c("Bacteria", "Firmicutes"),
c("Bacteria", "Firmicutes", "Bacilli", "Lactobacillales",
"Leuconostocaceae", "Weissella"),
c("Bacteria", "Firmicutes", "Clostridia", "Clostridiales",
"Peptococcaceae"))
# Prototype BIOM object without data
b <- list(type = "OTU table", shape=c(5, 5))
b$rows <- mapply(
function (x, y) list(id=x, metadata=list(taxonomy=y)),
b_otu_ids, b_taxonomy, SIMPLIFY=FALSE, USE.NAMES=FALSE)
b$columns <- lapply(b_sample_ids, function (x) list(id=x, metadata=NULL))
# BIOM object in dense format
db <- b
db$matrix_type <- "dense"
db$data <- list(
c(5, 10, 2, 0, 3),
c(76, 23, 28, 43, 56),
c(2, 1, 0, 0, 0),
c(637, 61, 63, 77, 34),
c(0, 0, 0, 1, 0))
# BIOM object in sparse format
sb <- b
sb$matrix_type <- "sparse"
sb$data <- list(
c(0, 0, 5), c(0, 1, 10), c(0, 2, 2), c(0, 4, 3),
c(1, 0, 76), c(1, 1, 23), c(1, 2, 28), c(1, 3, 43), c(1, 4, 56),
c(2, 0, 2), c(2, 1, 1),
c(3, 0, 637), c(3, 1, 61), c(3, 2, 63), c(3, 3, 77), c(3, 4, 34),
c(4, 3, 1))
context('biom_raw_data, dense format')
test_that("OTU IDs are parsed correctly", {
expect_equal(rownames(biom_raw_data(db)), b_otu_ids)
})
test_that("Sequence IDs are parsed correctly", {
expect_equal(colnames(biom_raw_data(db)), b_sample_ids)
})
test_that("OTU counts are correct", {
expect_equal(
biom_raw_data(db)["denovo0",],
structure(c(5, 10, 2, 0, 3), names=b_sample_ids))
expect_equal(
biom_raw_data(db)[,"A.1"],
structure(c(5, 76, 2, 637, 0), names=b_otu_ids))
})
context('biom_raw_data, sparse format')
test_that("OTU IDs are present", {
expect_equal(levels(biom_raw_data(sb)$OTU), b_otu_ids)
})
test_that("Sequence IDs are present", {
expect_equal(levels(biom_raw_data(sb)$SampleID), b_sample_ids)
})
test_that("OTU counts are in the same order as the biom file", {
expect_equal(
biom_raw_data(sb)$value,
c(5, 10, 2, 3, 76, 23, 28, 43, 56, 2, 1, 637, 61, 63, 77, 34, 1))
})
test_that("Values are correct if OTUs/samples do not appear in data", {
ssb <- sb
ssb$data <- ssb$data[8:11]
expect_equal(
biom_raw_data(ssb),
data.frame(
OTU=c("denovo1", "denovo1", "denovo2", "denovo2"),
SampleID=c("B.2", "C.1", "A.1", "A.2"),
value=c(43, 56, 2, 1)))
})
context('biom_taxonomy')
test_that("Taxonomy is correct", {
expect_equal(biom_taxonomy(sb)[[1]], "Bacteria")
})
test_that("Taxonomy list is labeled with OTU IDs", {
expect_equal(biom_taxonomy(sb)[["denovo2"]], c("Bacteria", "Firmicutes"))
})
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