tests/testthat/test-describ.R

In wenjie1991/CellBarcode: Cellular DNA Barcode Analysis toolkit

## set up a dummy data set
d1 <- data.frame(
  seq = c(
    "ACTTCGATCGATCGAAAAGATCGATCGATC",
    "AATTCGATCGATCGAAGAGATCGATCGATC",
    "CCTTCGATCGATCGAAGAAGATCGATCGATC",
    "TTTTCGATCGATCGAAAAGATCGATCGATC",
    "AAATCGATCGATCGAAGAGATCGATCGATC",
    "CCCTCGATCGATCGAAGAAGATCGATCGATC",
    "GGGTCGATCGATCGAAAAGATCGATCGATC",
    "GGATCGATCGATCGAAGAGATCGATCGATC",
    "ACTTCGATCGATCGAACAAGATCGATCGATC",
    "GGTTCGATCGATCGACGAGATCGATCGATC",
    "GCGTCCATCGATCGAAGAAGATCGATCGATC"
    ),
  freq = c(
    30, 60, 9, 10, 14, 5, 10, 30, 6, 4 , 6
    )
  )


d2 <- data.frame(
  seq = c(
    "ACTTCGATCGATCGAAAAGATCGATCGATC",
    "AATTCGATCGATCGAAGAGATCGATCGATC",
    "CCTTCGATCGATCGAAGAAGATCGATCGATC",
    "TTTTCGATCGATCGAAAAGATCGATCGATC",
    "AAATCGATCGATCGAAGAGATCGATCGATC",
    "CCCTCGATCGATCGAAGAAGATCGATCGATC",
    "GGGTCGATCGATCGAAAAGATCGATCGATC",
    "GGATCGATCGATCGAAGAGATCGATCGATC",
    "ACTTCGATCGATCGAACAAGATCGATCGATC",
    "GGTTCGATCGATCGACGAGATCGATCGATC",
    "GCGTCCATCGATCGAAGAAGATCGATCGATC"
    ),
  freq = c(
    30, 60, 9, 10, 14, 5, 10, 30, 6, 4 , 6
    )
  )


d_l <- list(test1 = d1, test2 = d2)

pattern <- "TCGATCGATCGA([ACTG]+)ATCGATCGATC"
bc_obj <- bc_extract(d_l, pattern, sample_name=c("test1", "test2"))
bc_obj <- bc_cure_depth(bc_obj, depth=6, isUpdate = FALSE)


test_that("barcode diversity", {
 
  expect_snapshot(
      bc_summary_barcode(bc_obj, plot = FALSE))

})