tests/testthat/test_ms1_plots.R

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

context("test: ms1_plots")

test_that("Testing ms1 plot plotting function", {

  # Download required test files------------------------------------------------

  source(system.file("tests/testthat/file_check.R", package = "pspecterlib"))
  downfolder <- file_check("downfolder")
  BU_ScanMetadata <- file_check("BU")

  # Test ms1 plot input checks--------------------------------------------------

  # ScanMetadata must be of the correct class
  expect_error(
    ms1_plots(data.frame(test = 1)),
    "ScanMetadata must be a scan_metadata object generated by get_scan_metadata."
  )

  # Scan number should be an integer
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = "5"
    ),
    "ScanNumber must be an integer."
  )

  # Scan number must be for a scan with an MS Level of 2
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 5
    ),
    "ScanNumber must be for a scan with an MS Level of 2."
  )

  # Window should be a single integer
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 31728,
      Window = c(2,3)
    ),
    "Window must be a single integer."
  )

  # Sequence should be a real sequence
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 31728,
      Sequence = "NOTREALSEQUENCE"
    ),
    "Sequence is not an acceptable input. See is_sequence."
  )

  # IsotopicPercentageFilter should be between 0 and 100
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 31728,
      IsotopicPercentageFilter = 150
    ),
    "The IsotopicPercentageFilter must be a number between 0-100."
  )

  # Interactive should be true or false
  expect_error(
    ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 31728,
      Interactive = "TRUE"
    ),
    "Interactive parameter must be either TRUE or FALSE."
  )

  # Create a ms1 bar plot-------------------------------------------------------

  # Make it static with negative isotopes and at the end of scan numbers
  suppressWarnings(thePlots1 <- ms1_plots(
    ScanMetadata = BU_ScanMetadata,
    ScanNumber = 34291,
    Interactive = NA
  ))
  expect_null(thePlots1[[2]])

  # Make it static without negative isotopes at the end of scan numbers with an
  # alternative sequence
  suppressWarnings(thePlots2 <- ms1_plots(
    ScanMetadata = BU_ScanMetadata,
    ScanNumber = 34291,
    Sequence = "TESTTESTTESTTESTTESTTESTTEST",
    Interactive = TRUE
  ))
  expect_null(thePlots2[[2]])

  # Make an example with a previous and next ms1 static
  suppressWarnings(thePlots3 <- ms1_plots(
    ScanMetadata = BU_ScanMetadata,
    ScanNumber = 31728,
    Interactive = FALSE
  ))
  expect_true(inherits(thePlots3[[1]], "ggplot"))


  # Make an example with a previous and next ms1 interactive
  suppressWarnings(thePlots4 <- ms1_plots(
    ScanMetadata = BU_ScanMetadata,
    ScanNumber = 31728
  ))
  expect_true(inherits(thePlots4[[1]], "plotly"))

  # Trigger a narrow window size
  suppressWarnings(suppressMessages(
    thePlots5 <- ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 31728,
      Window = 1,
      Interactive = FALSE
    )
  ))
  expect_true(inherits(thePlots5[[1]], "ggplot"))

  # Trigger a multiple sequence message
  suppressWarnings(suppressMessages(
    thePlots6 <- ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 29135,
      Interactive = FALSE
    )
  ))
  expect_true(inherits(thePlots6[[1]], "ggplot"))

  # Trigger a no sequence assigned example
  suppressWarnings(suppressMessages(
    thePlots7 <- ms1_plots(
      ScanMetadata = BU_ScanMetadata,
      ScanNumber = 29128,
      Interactive = FALSE
    )
  ))
  expect_true(inherits(thePlots7[[1]], "ggplot"))

})