tests/testthat/test_markers.R

In pRoloc: A unifying bioinformatics framework for spatial proteomics

context("organelle markers")


test_that("adding markers", {
    set.seed(1)
    x2 <- x <- new("MSnSet",
                   exprs = matrix(1, ncol = 4, nrow = 10,
                       dimnames = list(1:10)),
                   featureData = new("AnnotatedDataFrame",
                       data = data.frame(
                           markers = rep(c("A", "B"), each = 5),
                           id = c(LETTERS[1:7], "A", "Z", "Z"),
                           id2 = c(letters[1:7], "A", "Z", "Z"))))
    m <- sample(paste0("ORG", 1:5), 26, replace = TRUE)
    names(m) <- LETTERS
    ## Error: Detected an existing 'markers' feature column.
    expect_error(addMarkers(x, n))
    fData(x)$markers <- NULL
    ## Error: No markers found. Are you sure that the feature names match?
    expect_error(addMarkers(x, n))
    ## Case 1 (default): using feature names (all match)
    featureNames(x2) <- LETTERS[1:10]
    fData(x2)$markers <- NULL
    x2 <- addMarkers(x2, m)
    expect_true(all(m[1:10] == fData(x2)$markers))
    ## Case 2: using an fcol
    x3 <- addMarkers(x, m, fcol = "id")
    expect_true(all(m[as.character(fData(x3)$id)] ==
                    fData(x3)$markers))
    ## Case 3: using fcol, with unknowns
    x4 <- addMarkers(x, m, fcol = "id2")
    expect_true(all(c(rep("unknown", 7), as.character(fData(x3)$markers[8:10]))
                    == fData(x4)$markers))
    ## Case 4: markers not present in featureNames/fcol
    names(m)[1:10] <- letters[1:10]
    x5 <- addMarkers(x, m, fcol = "id")
    expect_true(all(c(rep("unknown", 8), as.character(fData(x3)$markers[9:10]))
                    == fData(x5)$markers))
})


test_that("vector and matrix markers", {
              data(dunkley2006)
              xx <- mrkVecToMat(dunkley2006)
              fData(xx)$markers <- NULL
              ## vec to mat and back keeps markers unchanged
              ## (as long as markers are for unique classes)
              expect_true(all.equal(fData(mrkMatToVec(xx))$Markers,
                                    fData(xx)$Markers))
              ## If non-unique, reverted to unknown when converting
              ## markers from matrix to vector
              fData(xx)$Markers[1:2, 2] <- 1
              yy <- mrkMatToVec(xx)
              expect_true(all(fData(xx)$markers[1:2] != "unknown"))
              expect_true(all(fData(yy)$markers[1:2] == "unknown"))
          })


test_that("sampling using vector and matrix markers", {
              data(tan2009r1)
              tan2009r1 <- mrkVecToMat(tan2009r1,
                                       vfcol = "PLSDA",
                                       mfcol = "MatPLSDA")
              smp1 <- sampleMSnSet(tan2009r1, fcol = "PLSDA", seed = 1L)
              smp2 <- sampleMSnSet(tan2009r1, fcol = "MatPLSDA", seed = 1L)
              expect_true(all.equal(featureNames(smp1), featureNames(smp2)))
          })

test_that("scer, scer_uniprot and scer_sgdb", {
              x <- pRolocmarkers("scer")
              xu <- pRolocmarkers("scer_uniprot")
              xs <- pRolocmarkers("scer_sgd")
              expect_true(all.equal(x, xu))
              ## names are different
              expect_true(all.equal(xu, xs, check.attributes=FALSE))
          })