tests/testthat/test_solveInt.R

In CNRGH/pintmf: Penalized Integrative Matrix Factorization for Multiomics Data

context("Penalized MF algorithm test: SolveInt")
set.seed(33)

rSpMatrix <- function(nrow, ncol, nnz,
                      rand.x = function(nnz) round(rnorm(nnz), 2))
{
  ## Purpose: random sparse matrix
  ## --------------------------------------------------------------
  ## Arguments: (nrow,ncol): dimension
  ##          nnz  :  number of non-zero entries
  ##         rand.x:  random number generator for 'x' slot
  ## --------------------------------------------------------------
  ## Author: Martin Maechler, Date: 14.-16. May 2007
  stopifnot((nnz <- as.integer(nnz)) >= 0,
            nrow >= 0, ncol >= 0, nnz <= nrow * ncol)
  spMatrix(nrow, ncol,
           i = sample(nrow, nnz, replace = TRUE),
           j = sample(ncol, nnz, replace = TRUE),
           x = rand.x(nnz))
}

W <- rbind(diag(1, nrow = 3, ncol = 3), diag(1, nrow = 3, ncol = 3))
H1 <- as.matrix(rSpMatrix(3, 100, nnz = 10, rand.x= function(nnz) round(rnorm(nnz, 2, 0.2), 2) ))
H2 <- as.matrix(rSpMatrix(3, 100, nnz = 10,  rand.x= function(nnz) round(rnorm(nnz, 2, 0.2), 2) ))
H3 <- as.matrix(rSpMatrix(3, 300, nnz = 10, rand.x= function(nnz) round(rnorm(nnz, 6, 0.2), 2) ))
Y1 <- as.matrix(W%*%H1 + rnorm(20, sd=1))
Y2 <- as.matrix(W%*%H2 + rnorm(20, sd=1))
Y3 <- as.matrix(W%*%H3 + rnorm(20, sd=1))
data <- list(Y1,Y2,Y3)
test_that("CPenalized MF algorithm test", {
  ## solving with PintMF
  R <- PintMF::SolveInt(Y=data, p=3, max.it=1, flavor_mod = "glmnet")
  expect_equal(is.list(R), TRUE)
  expect_equal(is.matrix(R$W), TRUE)
  expect_equal(is.list(R$H), TRUE)
  R <- PintMF::SolveInt(Y=data, p=3, max.it=1, flavor_mod = "ncvreg")
  expect_equal(is.list(R), TRUE)
  expect_equal(is.matrix(R$W), TRUE)
  expect_equal(is.list(R$H), TRUE)
})

test_that("CPenalized MF algorithm test supervised", {
  ## solving with PintMF
  group <- apply(W, 1, which.max)
  R <- PintMF::SolveInt(Y=data, p=3, max.it=3, flavor_mod = "glmnet", group=group)
  expect_equal(is.list(R), TRUE)
  expect_equal(is.matrix(R$W), TRUE)
  expect_equal(is.list(R$H), TRUE)
})