tests/testthat/test_115dimension_reduction.R

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

start <- as.POSIXlt(Sys.time())
context("115dimension_reduction.R")

## 2017-12, exported functions in model_pca:
## pca_information() pca_highscores() pcRes() plot_pca()
## plot_pcs() test_pca_methods()

pombe_expt <- make_pombe_expt(annotation = FALSE)

testing <- pca_information(pombe_expt, plot_pcas = TRUE,
                           expt_factors = c("strain", "minute", "replicate"))
expected <- c(94.15, 4.61, 0.79, 0.12, 0.11, 0.08)
actual <- head(testing[["rsquared_table"]][["prop_var"]])
test_that("pca_information() provides a rsquared table?", {
  expect_equal(expected, actual)
})

## I changed this to default to means vs. medians.
testing <- pca_highscores(pombe_expt)
expected <- c(-2.538439, -2.853661, 1.458443, -11.445837, -5.929639, -5.814761)
actual <- head(as.numeric(testing[["scores"]][, "Comp.1"]))
## 02
test_that("pca_highscores() provides some scores by PC?", {
  expect_equal(expected, actual, tolerance = 0.01)
})

testing <- plot_pca(pombe_expt)
expected <- c(6008536.5, 1329859.1, 550763.0, 214403.7, 203382.4, 176304.0)
actual <- head(testing[["result"]][["d"]])
test_that("plot_pca() provides expected SVD data?", {
  expect_equal(expected, actual, tolerance = 1.0)
})

test_that("plot_pca() provides a plot!?", {
  expect_equal(class(testing[["plot"]])[1], "gg")
})

expected <- c(-0.007178318, 0.070735209, -0.136645507, -0.374502211, 0.072181094, -0.028458656)
actual <- head(testing[["table"]])$PC1
test_that("We acquire expected values for PC1?", {
  expect_equal(expected, actual)
})

expected <- c(0.20199545, -0.19923795, -0.10775070, 0.28537150, -0.06148581, -0.25190759)
actual <- head(testing[["table"]])[["PC2"]]
test_that("We acquire expected values for PC2?", {
  expect_equal(expected, actual)
})

expected <- c(94.15, 4.61, 0.79, 0.12, 0.11, 0.08)
actual <- head(testing[["prop_var"]])
test_that("We get variances from pcRes?", {
  expect_equal(expected, actual)
})

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 115model_pca.R in ", elapsed,  " seconds.")