tests/testthat/test-queryKNN.R

In LTLA/BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages

# library(testthat); library(BiocNeighbors); source("setup.R"); source("test-queryKNN.R")

set.seed(999999)

test_that("queryKNN works with basic options", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    out <- queryKNN(Y, Z, k=8)
    ref <- refQueryKNN(Y, Z, k=8)
    expect_equal(out, ref)

    out <- queryKNN(Y, Z, k=8, BNPARAM=KmknnParam(distance="Manhattan"))
    ref <- refQueryKNN(Y, Z, k=8, type="manhattan")
    expect_equal(out, ref)

    out <- queryKNN(Y, Z, k=8, BNPARAM=KmknnParam(distance="Cosine"))
    Y1 <- Y/sqrt(rowSums(Y^2))
    Z1 <- Z/sqrt(rowSums(Z^2))
    ref <- queryKNN(Y1, Z1, k=8)
    expect_equal(out, ref)
})

test_that("queryKNN works in parallel", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    out <- queryKNN(Y, Z, k=8)
    pout <- queryKNN(Y, Z, k=8, num.threads=2)
    expect_equal(out, pout)

    pout <- queryKNN(Y, Z, k=8, BPPARAM=BiocParallel::SnowParam(2))
    expect_equal(out, pout)
})

test_that("queryKNN works with subsets", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    out <- queryKNN(Y, Z, k=8)
    sout <- queryKNN(Y, Z, subset=1:10, k=8)
    out$index <- out$index[1:10,]
    out$distance <- out$distance[1:10,]
    expect_equal(out, sout)

    expect_warning(out <- queryKNN(Y[0,,drop=FALSE], Z, k=8), "capped")
    expect_identical(dim(out$index), c(nrow(Z), 0L))
    expect_identical(dim(out$distance), c(nrow(Z), 0L))
})

test_that("queryKNN works with variable k", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    k <- rep(c(4, 10), length.out=nrow(Z))
    out <- queryKNN(Y, Z, k=k)

    keep <- k == 4
    ref <- queryKNN(Y, Z, k=4)
    expect_identical(do.call(rbind, out$index[keep]), ref$index[keep,])
    expect_identical(do.call(rbind, out$distance[keep]), ref$distance[keep,])

    keep <- k == 10
    ref <- queryKNN(Y, Z, k=10)
    expect_identical(do.call(rbind, out$index[keep]), ref$index[keep,])
    expect_identical(do.call(rbind, out$distance[keep]), ref$distance[keep,])

    # The AsIs forced variable works.
    out <- queryKNN(Y, Z, k=I(10), subset=1)
    ref <- queryKNN(Y, Z, k=10, subset=1)
    expect_identical(out$index[[1]], ref$index[1,])
    expect_identical(out$distance[[1]], ref$distance[1,])
})

test_that("queryKNN works with prebuilt indices", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    built <- buildIndex(Y, k=8)
    out <- queryKNN(Y, Z, k=8)
    preout <- queryKNN(built, Z, k=8)
    expect_identical(out, preout)

    # Unaffected by BNPARAM settings at this point.
    preout <- queryKNN(built, Z, k=8, BNPARAM=AnnoyParam())
    expect_identical(out, preout)

    # Throws an error for deserialized prebuilt indices.
    tmp <- tempfile(fileext=".rds")
    saveRDS(built, tmp)
    expect_error(queryKNN(readRDS(tmp), Z, k=1), "null pointer")
})

test_that("queryKNN works when inputs are transposed", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    out <- queryKNN(Y, Z, k=8)
    tout <- queryKNN(t(Y), t(Z), k=8, transposed=TRUE)
    expect_identical(out, tout)
})

test_that("queryKNN works with variable outputs", {
    Y <- matrix(rnorm(10000), ncol=20)
    Z <- matrix(rnorm(2000), ncol=20)

    out <- queryKNN(Y, Z, k=8)

    iout <- queryKNN(Y, Z, k=8, get.distance=FALSE)
    expect_null(iout$distance)
    expect_identical(iout$index, out$index)

    dout <- queryKNN(Y, Z, k=8, get.index=FALSE)
    expect_null(dout$index)
    expect_identical(dout$distance, out$distance)

    tout <- queryKNN(Y, Z, k=8, get.index="transposed", get.distance="transposed")
    expect_identical(t(tout$distance), out$distance)
    expect_identical(t(tout$index), out$index)
})