tests/testthat/test_topseq.R

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

context("Find n top sequences with highest frequency")
library(LymphoSeq2)
library(tidyverse)

test_that("Find top sequence in all samples", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/015V06013979_CFAR.tsv", threads = 1)
  atable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction_aa")
  ttable <- LymphoSeq2::topSeqs(atable, top = 1) %>%
    dplyr::pull(duplicate_frequency) %>%
    base::max()
  ctable <- atable %>%
    dplyr::pull(duplicate_frequency) %>%
    base::max()
  expect_equal(ctable, ttable)
})

test_that("Find the top ten sequences in one sample", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/015V06013979_CFAR.tsv", threads = 1)
  atable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction_aa")
  ttable <- LymphoSeq2::topSeqs(atable, top = 10) %>%
    dplyr::pull(duplicate_frequency)
  ctable <- atable %>%
    dplyr::pull(duplicate_frequency) %>%
    base::unique() %>%
    base::sort(decreasing = TRUE)
  expect_equal(ctable[1:10], ttable)
})


test_that("Top sequences across samples is correctly identified", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/", threads = 1)
  atable <- LymphoSeq2::productiveSeq(stable, aggregate = "junction_aa")
  ttable <- LymphoSeq2::topSeqs(atable, top = 1)

  ctable <- atable %>%
    dplyr::group_by(repertoire_id) %>%
    dplyr::group_split(.keep = TRUE) %>%
    purrr::map(LymphoSeq2::topSeqs) %>%
    dplyr::bind_rows()
  expect_true(base::all.equal(ctable, ttable))
})