tests/testthat/test-geom_subgene_arrow.R

In gggenes: Draw Gene Arrow Maps in 'ggplot2'

context("geom_subgene_arrow")

test_that("a simple geom_subgene_arrow plot is drawn without errors", {
  expect_no_error( {
    library(ggplot2)
    p <- ggplot(
      example_genes,
      aes(xmin = start, xmax = end, y = molecule, forward = orientation)
    ) +
      geom_gene_arrow() +
      geom_subgene_arrow(
        data = example_subgenes,
        aes(
          xmin = start,
          xmax = end,
          y = molecule,
          fill = gene,
          xsubmin = from,
          xsubmax = to,
          forward = orientation
        )
      ) +
      facet_wrap(~ molecule, scales = "free", ncol = 1) +
      theme_genes()
    print(p)
  } )

  expect_doppelganger(title = "Basic plot with subgenes", fig = {
    ggplot(
      example_genes,
      aes(xmin = start, xmax = end, y = molecule, forward = orientation)
    ) +
      geom_gene_arrow() +
      geom_subgene_arrow(
        data = example_subgenes,
        aes(
          xmin = start,
          xmax = end,
          y = molecule,
          fill = gene,
          xsubmin = from,
          xsubmax = to,
          forward = orientation
        )
      ) +
      facet_wrap(~ molecule, scales = "free", ncol = 1) +
      theme_genes()

  })

})

test_that("boundary breaking subgenes are caught", {
  ## only 1 valid subgene
  genes <- data.frame(
    gene = c("cds1", "cd2", "cd3", "cds4"),
    start = c(2000, 2000, 2050, 2050),
    end = c(1000, 1000, 3000, 3000),
    subgenestart =  c(1200, 1000, 2000, 2800),
    subgeneend = c(1000, 600, 2200, 3200))

    expect_warning(
      print(plt <- ggplot(genes, aes(xmin = start, xmax = end, y = "strand")) +
                        geom_gene_arrow() +
                        geom_subgene_arrow(aes(xsubmin = subgenestart,
                                       xsubmax = subgeneend), fill = "blue")),
      regex="Subgene 2.*Subgene 3.*Subgene 4"
    )

    expect_is(plt, "ggplot")
})