tests/testthat/test-EpivizMetagenomicsInnerNodeData_class.R

In metavizr: R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

context("testing EpivizMetagenomicsInnerNodesData Class")
library(curatedMetagenomicData)

# From curatedMetagenomicData and MicrobiomeWorkshop Vignettes
loman_file <- system.file("extdata", "loman.RData", package = "metavizr")
load(loman_file)
loman.eset <- loman[[1]]
loman_MR <- ExpressionSet2MRexperiment(loman.eset)
feature_order <- colnames(fData(loman_MR))
mObj <- metavizr:::EpivizMetagenomicsDataInnerNodes$new(loman_MR, feature_order = feature_order)

test_that("getValuesInnerNodes", {
  sampleId<- "OBK1122"
  res <- mObj$getValues(measurements = sampleId)
  
  expected <- c(0.000 , 0.000, 1.2948, 499.0848, 0.000, 89.1858, 0.000, 0.000, 0.000, 0.000, 7.7368, 0.000, 0.000, 0.000, 0.000)
  diff_result <- setdiff(round(unname(res[[sampleId]]), digits=3), round(expected,digits=3))
  expect_equal(length(diff_result), 0)
})

test_that("getHierarchyInnerNodesRoot", {
  res <- mObj$getHierarchy(nodeId = NULL)
  
  expect_equal("AllFeatures", as.character(res$tree$label))
  expect_equal(3, res$tree$nchildren)
})

test_that("getRowsInnerNodes", {
  sampleId<- "OBK1122"
  resRows <- mObj$getRows(measurement = sampleId, selectedLevels = 2)  
  expected_label <- c("Euryarchaeota", "Actinobacteria", "Bacteroidetes", 
                      "Firmicutes", "Fusobacteria", "Proteobacteria", 
                      "Verrucomicrobia", "Viruses_noname")
  
  intersect_result <- intersect(resRows$metadata$label, expected_label)
  expect_equal(length(intersect_result), length(expected_label))
})