tests/testthat/test_Gviz-methods.R

In Gviz: Plotting data and annotation information along genomic coordinates

## Gviz methods

test_that("General accessors work", {

    expect_identical(ranges(dataTrack), granges(gr))
    expect_identical(range(dataTrack), ir)

    expect_identical(ranges(axisTrack), gr)
    expect_identical(range(axisTrack), ir)

    expect_identical(seqnames(annoTrack), "chr1")
    expect_identical(seqnames(dataTrack), "chr1")
    expect_identical(seqnames(seqTrack.dna), "chr1")
    expect_identical(seqnames(seqTrack.rna), "chr1")
    expect_identical(seqnames(seqTrack.bs), seqnames(BSgenome.Hsapiens.UCSC.hg19))

    expect_identical(seqlevels(annoTrack), "chr1")
    expect_identical(seqlevels(dataTrack), "chr1")
    expect_identical(seqlevels(seqTrack.dna), "chr1")
    expect_identical(seqlevels(seqTrack.rna), "chr1")
    expect_identical(seqlevels(seqTrack.bs), seqlevels(BSgenome.Hsapiens.UCSC.hg19))

    expect_identical(seqinfo(annoTrack), table("chr1"))

    expect_identical(min(dataTrack), 1L)
    expect_identical(max(dataTrack), 5L)

    expect_identical(start(dataTrack), 1L)
    expect_identical(end(dataTrack), 5L)
    expect_identical(width(dataTrack), 5L)
    expect_identical(length(dataTrack), 1L)

    expect_identical(start(ideoTrack), NULL)
    expect_identical(end(ideoTrack), NULL)
    expect_identical(width(ideoTrack), NULL)
    expect_identical(length(ideoTrack), 4L)

    expect_identical(start(axisTrack), 1L)
    expect_identical(end(axisTrack), 5L)
    expect_identical(width(axisTrack), 5L)

    expect_identical(start(seqTrack.dna), NULL)
    expect_identical(end(seqTrack.dna), NULL)
    expect_identical(width(seqTrack.dna), NULL)
    expect_identical(length(seqTrack.dna), 100L) # !

    expect_identical(length(highTrack), 1L)
    expect_identical(length(overTrack), 2L)
})

test_that("General replacement methods work", {
    ranges(dataTrack) <- gr2
    expect_identical(ranges(dataTrack), gr2)
    expect_identical(range(dataTrack), ir2)

    ranges(axisTrack) <- gr2
    expect_identical(ranges(axisTrack), gr2)
    expect_identical(range(axisTrack), ir2)

    ranges(annoTrack) <- gr2
    expect_identical(ranges(annoTrack), gr2)
    expect_identical(range(annoTrack), ir2)

    start(annoTrack) <- 3L
    expect_identical(start(annoTrack), 3L)
    start(axisTrack) <- 3L
    expect_identical(start(axisTrack), 3L)
    start(ideoTrack) <- 3L
    expect_identical(start(ideoTrack), NULL)

    end(annoTrack) <- 4L
    expect_identical(end(annoTrack), 4L)
    end(axisTrack) <- 4L
    expect_identical(end(axisTrack), 4L)
    end(ideoTrack) <- 4L
    expect_identical(end(ideoTrack), NULL)

    width(annoTrack) <- 10L
    expect_identical(width(annoTrack), 10L)

    width(ideoTrack) <- 10L
    expect_identical(ideoTrack, ideoTrack)
})

test_that("values accessors and replacement methods work", {
    expect_identical(values(annoTrack), data.frame(feature = "unknown", group = "1",
                                                   id = "unknown", density = 1, stringsAsFactors=FALSE))
    expect_identical(values(axisTrack), data.frame(score = 1, stringsAsFactors=FALSE))
    expect_identical(values(dataTrack), as.matrix(c(score = 1)))
    expect_identical(values(DataTrack()), matrix(logical(), 0, 0))
    expect_identical(values(alnTrack), NULL)

    values(dataTrack) <- matrix(3, dimnames=list("score", NULL))
    expect_identical(values(dataTrack), as.matrix(c(score = 3)))
    values(dataTrack) <- 3
    expect_identical(values(dataTrack), as.matrix(c(3)))
    expect_error(values(dataTrack) <- matrix("3", dimnames=list("score", NULL)), "Not numeric or dimensions of replacement value do not match.")
    expect_error(values(dataTrack) <- c(3,3), "Not numeric or invalid length of replacement vector.")

})

test_that("subseq works", {
    expect_error(subseq(SequenceTrack(), start=NA, end=NA, width=3), "Two out of the three in")
    expect_error(subseq(SequenceTrack(), start=10, end=1), "'end' has to be bigger than 'start'")
    expect_error(subseq(seqTrack.dna, start=10, end=1), "'end' has to be bigger than 'start'")
    expect_error(subseq(SequenceTrack(), start=1, end=10e6+2), "Sequence is too big")
    expect_error(subseq(seqTrack.bs, start=1, end=10e6+2), "Sequence is too big")
    expect_warning(subseq(seqTrack.dna, start=1, end=10, width=10), "are provided, ignoring")
    expect_identical(as.character(subseq(SequenceTrack(), start=1, end=10)), as.character(DNAString("----------")))
    expect_identical(as.character(subseq(seqTrack.dna, start=1, end=10)), as.character(DNAString("ATTTCCCTGA")))
    expect_identical(as.character(subseq(seqTrack.dna, start=1, width=10)), as.character(DNAString("ATTTCCCTGA")))
    expect_identical(as.character(subseq(seqTrack.dna, end=10, width=10)), as.character(DNAString("ATTTCCCTGA")))
    expect_identical(as.character(subseq(seqTrack.dna, start=91, end=110)), as.character(DNAString("ACGTCTTCCA----------")))
    expect_identical(as.character(subseq(seqTrack.bs, start=1, width=10)), as.character(DNAString("NNNNNNNNNN")))
    expect_identical(as.character(subseq(seqTrack.dna, start=1)), as.character(dna.sq[[1]]))
    expect_identical(as.character(subseq(SequenceTrack(), start=1)), as.character(DNAString("-")))
    expect_identical(as.character(subseq(seqTrack.dna, end=1)), as.character(DNAString("A")))
    expect_identical(as.character(subseq(SequenceTrack(), end=1)), as.character(DNAString("-")))
    displayPars(seqTrack.dna)$complement <- TRUE
    expect_identical(as.character(subseq(seqTrack.dna, start=1, end=10)), as.character(DNAString("TAAAGGGACT")))


    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1")), "at least two out of ")
    expect_error(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1), "at least two out of ")
    expect_warning(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, end=10, width=10)), "All ")
    expect_error(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=NA, end=NA, width=10)), "Two ")
    expect_identical(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, width=10)), as.character(DNAString("CTANGAGACG")))
    expect_identical(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), end=10, width=10)), as.character(DNAString("CTANGAGACG")))
    ## expect_identical(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, end=NA, width=10)), as.character(DNAString("CTANGAGACG")))
    expect_identical(as.character(subseq(SequenceTrack(fastafile, chromosome="chr1"), start=1, end=10)), as.character(DNAString("CTANGAGACG")))
})

test_that("chromosome accessors and replacement methods work", {
    expect_identical(chromosome(annoTrack), "chr1")
    chromosome(annoTrack) <- "chr2"
    expect_identical(chromosome(annoTrack), "chr2")

    expect_identical(chromosome(dataTrack), "chr1")

    expect_identical(chromosome(seqTrack.dna), "chr1")
    chromosome(seqTrack.dna) <- "chr2"
    expect_identical(chromosome(seqTrack.dna), "chr2")

    expect_identical(chromosome(ideoTrack), "chrI")
    chromosome(ideoTrack) <- "chrII"
    expect_identical(chromosome(ideoTrack), "chrII")

    expect_identical(chromosome(highTrack), "chr1")
    chromosome(highTrack) <- "chr2"
    expect_identical(chromosome(highTrack), "chr2")

    expect_identical(chromosome(overTrack), "chr1")
    chromosome(overTrack) <- "chr2"
    expect_identical(chromosome(overTrack), "chr2")

    expect_identical(chromosome(axisTrack), NULL)
    chromosome(axisTrack) <- "chr1"
    expect_identical(chromosome(axisTrack), NULL)

    expect_identical(chromosome(alnTrack), "chrNA")
    chromosome(alnTrack) <- "chr1"
    expect_identical(chromosome(alnTrack), "chr1")

})


test_that("genome accessors and replacement methods work", {
    expect_identical(is.na(genome(annoTrack)), TRUE)
    genome(annoTrack) <- "hg38"
    expect_identical(genome(annoTrack), "hg38")

    expect_identical(is.na(genome(seqTrack.dna)), TRUE)
    ## genome(seqTrack.dna) <- "hg38"
    ## expect_identical(genome(seqTrack.dna), "hg38")

    expect_identical(genome(ideoTrack), "sacCer3")
    ## genome(ideoTrack) <- "sacCer2"
    ## expect_identical(genome(ideoTrack), "sacCer2")

    expect_identical(genome(overTrack), NULL)
    genome(overTrack) <- "hg38"
    expect_identical(genome(overTrack), NULL)
})

test_that("strand accessors and replacement methods work", {
    expect_identical(strand(dataTrack), "*")
    strand(dataTrack) <- "+"
    expect_identical(strand(dataTrack), "+")
    expect_error(strand(dataTrack) <- rep("+", 2), "Invalid")

    expect_identical(strand(annoTrack), "*")
    strand(annoTrack) <- "+"
    expect_identical(strand(annoTrack), "+")

    expect_identical(strand(axisTrack), "*")

    annoTrack <- AnnotationTrack(c(gr,gr2))
    expect_identical(strand(annoTrack), rep("*", 2))
    strand(annoTrack) <- rep("+", 2)
    expect_identical(strand(annoTrack), rep("+", 2))
    expect_error(strand(annoTrack) <- rep("+", 3), "Invalid replacement value or length of replacement")
})

test_that("subsetting with [ works", {
    expect_identical(annoTrack[1]@range, GRanges("chr1", IRanges(1,5), feature="unknown", group="1", id="unknown", density=1))
    expect_error(annoTrack[2], "subscript contains out-of-bounds")

    expect_identical(axisTrack[1]@range, GRanges("chr1", IRanges(1,5), score=1))
    expect_error(dataTrack[2], "subscript out of bounds")

    expect_identical(ideoTrack[1], ideoTrack)

    expect_identical(dataTrack[1,,]@range, GRanges("chr1", IRanges(1,5)))
    expect_error(dataTrack[2], "subscript out of bounds")
    expect_identical(dataTrack[,1,]@data, matrix(1, nrow=1, dimnames=list("score", NULL)))
    expect_error(dataTrack[,2,]@data, "subscript contains out-of-bounds indices")
})

test_that("splitting works", {
    aTrack <- AnnotationTrack(c(gr, gr2))
    expect_identical(names(split(aTrack, f=c("a", "b"))), c("a", "b"))
    expect_identical(split(aTrack, f=c("a", "b"))[[1]]@range, aTrack@range[1])
    expect_identical(split(aTrack, f=c("a", "b"))[[2]]@range, aTrack@range[2])

    dTrack <- DataTrack(c(gr, gr2))
    expect_identical(names(split(dTrack, f=c("a", "b"))), c("a", "b"))
    expect_identical(split(dTrack, f=c("a", "b"))[[1]]@range, dTrack@range[1])
    expect_identical(split(dTrack, f=c("a", "b"))[[1]]@data, dTrack@data[,1, drop=FALSE])
    expect_identical(split(dTrack, f=c("a", "b"))[[2]]@range, dTrack@range[2])
    expect_identical(split(dTrack, f=c("a", "b"))[[2]]@data, dTrack@data[,2, drop=FALSE])
})

test_that("names accessors and replacement methods work", {
    expect_identical(names(annoTrack), "AnnotationTrack")
    names(annoTrack) <- "AnnoTrack"
    expect_identical(names(annoTrack), "AnnoTrack")
})

test_that("gene, symbol, transcript, feature and exon accessors and replacement methods work", {
    expect_identical(gene(geneTrack), as.character(geneModels$gene))
    gene(geneTrack) <- paste0(as.character(geneModels$gene), ".1")
    expect_identical(gene(geneTrack), paste0(as.character(geneModels$gene), ".1"))

    expect_identical(symbol(geneTrack), as.character(geneModels$symbol))
    symbol(geneTrack) <- paste0(as.character(geneModels$symbol), ".1")
    expect_identical(symbol(geneTrack), paste0(as.character(geneModels$symbol), ".1"))

    expect_identical(transcript(geneTrack), as.character(geneModels$transcript))
    transcript(geneTrack) <- paste0(as.character(geneModels$transcript), ".1")
    expect_identical(transcript(geneTrack), paste0(as.character(geneModels$transcript), ".1"))

    expect_identical(exon(geneTrack), as.character(geneModels$exon))
    exon(geneTrack) <- paste0(as.character(geneModels$exon), ".1")
    expect_identical(exon(geneTrack), paste0(as.character(geneModels$exon), ".1"))

    expect_identical(feature(geneTrack), as.character(geneModels$feature))
    feature(geneTrack) <- paste0(as.character(geneModels$feature), ".1")
    expect_identical(feature(geneTrack), paste0(as.character(geneModels$feature), ".1"))

    expect_identical(feature(dataTrack), NULL)
    feature(dataTrack) <- "1"
    expect_identical(dataTrack, dataTrack)
})

test_that("group and identifier accessors and replacement methods work", {
    expect_identical(group(geneTrack), as.character(geneModels$transcript))
    group(geneTrack) <- paste0(as.character(geneModels$transcript), ".1")
    expect_identical(group(geneTrack), paste0(as.character(geneModels$transcript), ".1"))

    expect_identical(group(dataTrack), NULL)

    expect_identical(identifier(geneTrack), as.character(geneModels$symbol))
    expect_identical(identifier(geneTrack, type=NULL), as.character(geneModels$symbol))
    identifier(geneTrack) <- paste0(as.character(geneModels$symbol), ".1")
    expect_identical(identifier(geneTrack), paste0(as.character(geneModels$symbol), ".1"))

    expect_identical(identifier(annoTrack), "1")
    expect_identical(identifier(annoTrack, type=NULL), "1")
    identifier(annoTrack) <- "1.1"
    expect_identical(identifier(annoTrack), "1.1")
})

test_that("stacking works", {
    expect_identical(stacking(annoTrack), "squish")
    stacking(annoTrack) <- "dense"
    expect_identical(stacking(annoTrack), "dense")

    expect_identical(stacks(annoTrack), NULL)
    expect_identical(stacks(alnTrack), 0)

    expect_identical(Gviz:::setStacks(AnnotationTrack(c(gr)))@stacks, c(unknown = 1L))
})


test_that("position calculation works", {
    expect_identical(position(annoTrack), 3)
    expect_identical(position(annoTrack, from=1, to=5), 3)
    expect_identical(position(annoTrack, from=10, to=15), numeric())
})


test_that("imageMap and coords work", {
    expect_identical(imageMap(annoTrack), NULL)
    im <- new("ImageMap",
              coords=matrix(1, ncol=4, nrow=1, dimnames=list("first")),
              tags=list(first=1))
    imageMap(annoTrack) <- im
    expect_identical(imageMap(annoTrack), im)

    expect_identical(coords(NULL), NULL)
    expect_identical(coords(im), matrix(1, ncol=4, nrow=1, dimnames=list("first")))
    expect_identical(coords(annoTrack), matrix(1, ncol=4, nrow=1, dimnames=list("first")))

    expect_identical(tags(NULL), NULL)
    expect_identical(tags(im), list(first=1))
    expect_identical(tags(annoTrack), list(first=1))
})

test_that("consolidating of tracks works", {
    expect_identical(chromosome(consolidateTrack(annoTrack, chromosome="chr2", alpha=TRUE)), "chr2")
    expect_identical(getPar(consolidateTrack(annoTrack, chromosome="chr2", alpha=TRUE), ".__hasAlphaSupport"), TRUE)
    expect_identical(getPar(consolidateTrack(annoTrack, chromosome="chr2", alpha=FALSE, size=2), "size"), 2)
})



test_that("collapsing of tracks works", {
    expect_identical(.myFindOverlaps(gr, gr2), c(queryHits = 1L))
    expect_identical(Gviz:::.myFindOverlaps(gr, GRanges("chr2", IRanges(1, 5))), integer())
})