tests/testthat/test-box.R

In LTLA/InteractionSet: Base Classes for Storing Genomic Interaction Data

# Testing the bounding box behaviour.
# library(InteractionSet); library(testthat); source("test-box.R")

set.seed(10000)
N <- 30
all.starts <- round(runif(N, 1, 100))
all.ends <- all.starts + round(runif(N, 5, 20))
all.regions <- GRanges(rep(c("chrA", "chrB"), c(N-10, 10)), IRanges(all.starts, all.ends))

Np <- 20
all.anchor1 <- sample(N, Np)
all.anchor2 <- sample(N, Np)
x <- GInteractions(all.anchor1, all.anchor2, all.regions)

# Setting up factors so that, within one level, all entries belong to the same chromosome.
all.chrs <- as.character(seqnames(regions(x)))

test_that("boundingBox works with a factor", {
    for (i in 1:3) { 
        f <- paste0(all.chrs[anchors(x, type="first", id=TRUE)],
                    all.chrs[anchors(x, type="second", id=TRUE)],
                    sample(i, Np, replace=TRUE))
    
        ref1 <- unlist(range(split(anchors(x, type="first"), f)))
        ref2 <- unlist(range(split(anchors(x, type="second"), f)))
        ref <- GInteractions(unname(ref1), unname(ref2))
        names(ref) <- names(ref1)
        expect_identical(ref, boundingBox(x, f))
    }
})

test_that("boundingBox works without a factor", {
    only.A <- all.chrs[anchors(x, type="first", id=TRUE)] == "chrA" & all.chrs[anchors(x, type="second", id=TRUE)] == "chrA"
    x.A <- x[only.A]
    ref1 <- range(anchors(x.A, type="first"))
    ref2 <- range(anchors(x.A, type="second"))
    ref <- GInteractions(unname(ref1), unname(ref2))
    names(ref) <- 1
    expect_identical(boundingBox(x.A), ref)

    only.AB <- all.chrs[anchors(x, type="first", id=TRUE)] == "chrA" & all.chrs[anchors(x, type="second", id=TRUE)] == "chrB"
    x.AB <- x[only.AB]
    ref1 <- range(anchors(x.AB, type="first"))
    ref2 <- range(anchors(x.AB, type="second"))
    ref <- GInteractions(unname(ref1), unname(ref2))
    names(ref) <- 1
    expect_identical(boundingBox(x.AB), ref)
})

test_that("boundingBox breaks with silly inputs", {
    expect_error(boundingBox(x), "multiple chromosomes for group '1'")
    f <- rep("whee", Np)
    f[-1] <- "YAY"
    expect_error(boundingBox(x,f), "multiple chromosomes for group 'YAY'")
    
    ref <- GInteractions(all.regions[0], all.regions[0])
    names(ref) <- character(0)
    expect_identical(boundingBox(x[0]), ref)
})