tests/testthat/test_consistency_getW.R

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

context("Consistency of the optimization algorithm: get.W")
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))
Ybar <- cbind(Y1, Y2, Y3)
Zbar <- cbind(H1, H2, H3) %>% t
group <- apply(W, 1, which.max)
test_that("Consistency of get.W", {
  ## solving with PintMF
  We <- PintMF::get.W(Zbar, Ybar)
  print(We)
  expect_equal(is.matrix(We), TRUE)
  expect_equal(ncol(We), ncol(W))
  expect_equal(nrow(We), nrow(W))
})



test_that("Consistency of get.W in supervised way", {
  ## solving with PintMF
  We <- PintMF::get.W.supervised(Zbar, Ybar, group=group)
  expect_equal(is.matrix(We), TRUE)
  expect_equal(ncol(We), ncol(W))
  expect_equal(nrow(We), nrow(W))
  print(We)
})