tests/testthat/test_hiloadings.R

In federicomarini/pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

test_that("Check that genes with hi loadings are extracted", {
  pcaobj <- prcomp(t(SummarizedExperiment::assay(rlt)))
  anno <- data.frame(gene_id = rownames(dds), 
                     gene_name = toupper(rownames(dds)), 
                     stringsAsFactors = FALSE, 
                     row.names = rownames(dds))
  
  hi_loadings(pcaobj, 1)
  
  expect_is(hi_loadings(pcaobj, 1, exprTable = counts(dds)), "matrix")
  expect_true(
    all(rownames(hi_loadings(pcaobj, 1, exprTable = counts(dds), annotation = NULL)) %in% rownames(dds))
  )
  expect_true(
    all(rownames(hi_loadings(pcaobj, 1, exprTable = counts(dds), annotation = anno)) %in% anno$gene_name)
  )
})