tests/testthat/test-scale_rows.R

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

context("scale_rows")

M <- list(
  wide = matrix(rnorm(50, mean = 1, sd = 2), nrow = 5,
                dimnames = list(LETTERS[1:5], letters[1:10])),
  long = matrix(rnorm(50, mean = 1, sd = 2), nrow = 10,
                dimnames = list(LETTERS[1:10], letters[1:5])),
  square = matrix(rnorm(100, mean = 1, sd = 2), nrow = 10,
                  dimnames = list(LETTERS[1:10], letters[1:10])))

test_that("scale and center are flags", {
  params <- expand.grid(center = c(TRUE, FALSE), scale = c(TRUE,FALSE))

  for (orientation in names(M)) {
    m <- M[[orientation]]
    for (i in seq(nrow(params))) {
      p <- params[i,,drop = FALSE]
      res <- scale_rows(m, center = p$center, scale = p$scale,
                        base.attributes = TRUE)
      ex <- t(scale(t(m), center = p$center, scale = p$scale))
      info <- paste(names(p), unname(unlist(p)), sep = ":", collapse = ",")
      expect_equal(res, ex, info = sprintf("%s (%s)", info, orientation))
    }
  }
})

test_that("centering on a subgroup of specified coloumns", {
  ctrl <- c("b", "d", "e")
  params <- expand.grid(scale = c(TRUE, FALSE))
  for (orientation in names(M)) {
    m <- M[[orientation]]
    means <- Matrix::rowMeans(m[, ctrl])
    for (i in seq(nrow(params))) {
      p <- params[i,,drop = FALSE]
      info <- paste(names(p), unname(unlist(p)), sep = ":", collapse = ",")
      info <- sprintf("%s (%s)", info, orientation)

      res <- scale_rows(m, center = ctrl, scale = p$scale,
                        base.attributes = TRUE)
      resi <- scale_rows(m, center = match(ctrl, colnames(m)), scale = p$scale,
                         base.attributes = TRUE)
      resl <- scale_rows(m, center = colnames(m) %in% ctrl, scale = p$scale,
                         base.attributes = TRUE)

      ex <- t(scale(t(m), center = means, scale = p$scale))

      expect_equal(res, ex, info = info)
      expect_equal(resi, ex, info = paste(info, "[by index]"))
      expect_equal(resl, ex, info = paste(info, "[by logical]"))
    }
  }
})

test_that("centering on pre-calculate values", {
  max.rows <- max(sapply(M, nrow))
  means.all <- setNames(rnorm(max.rows), sample(head(LETTERS, max.rows)))

  params <- expand.grid(scale = c(TRUE, FALSE))
  for (orientation in names(M)) {
    m <- M[[orientation]]
    means <- means.all[rownames(m)]
    for (i in seq(nrow(params))) {
      p <- params[i,,drop = FALSE]
      info <- paste(names(p), unname(unlist(p)), sep = ":", collapse = ",")
      info <- sprintf("%s (%s)", info, orientation)

      res <- scale_rows(m, center = means, scale = p$scale,
                        base.attributes = TRUE)
      ex <- t(scale(t(m), center = means, scale = p$scale))

      expect_equal(res, ex, info = info)
    }
  }
})