tests/testthat/test-visualize_MSA_using_ggmsa.R

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

test_that("msa works with both msa, set and file", {
  aln <- Biostrings::readAAMultipleAlignment("phmmer_example.afa")
  vdiffr::expect_doppelganger("A msa",
      visualize_MSA_using_ggmsa(aln,
         start = 100,
         end = 115,
         color_scheme = "Chemistry_AA",
         max_positions_per_row = 5,
         alignment_index = c(1:4))
      )
  vdiffr::expect_doppelganger("A msa",
    visualize_MSA_using_ggmsa("phmmer_example.afa",
                              start = 100,
                              end = 115,
                              color_scheme = "Chemistry_AA",
                              max_positions_per_row = 5,
                              alignment_index = c(1:4))
  )
  vdiffr::expect_doppelganger("A msa",
  visualize_MSA_using_ggmsa(Biostrings::AAStringSet(aln),
                            start = 100,
                            end = 115,
                            color_scheme = "Chemistry_AA",
                            max_positions_per_row = 5,
                            alignment_index = c(1:4))
)
})