tests/testthat/test_coverage_plot.R

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

context("test: coverage_plot")

test_that("Testing coverage plot plotting function", {

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

  PC <- readRDS(system.file("testdata", "PeptideCoverage.RDS", package = "pspecterlib"))

  # Test coverage plot input checks---------------------------------------------

  # Peptide coverage must be of the correct class
  expect_error(
    coverage_plot(data.frame(test = 1)),
    "PeptideCoverage must be an object of the peptide_coverage class generated by get_peptide_coverage."
  )

  # Color by score must indicate the score to color by
  expect_error(
    coverage_plot(PC, ColorByScore = c("QValue", "Score")),
    "ColorByScore should be a single character or NULL."
  )

  # Color by score must be an acceptable input
  expect_error(
    coverage_plot(PC, ColorByScore = "test"),
    'Acceptable values for ColorByScore are "QValue" or "Score."'
  )

  # Interactive must be a logical input
  expect_error(
    coverage_plot(PC, Interactive = "FALSE"),
    "Interactive must be a single logical value TRUE or FALSE."
  )

  # Create a coverage plot------------------------------------------------------

  # Create a static plot with no colorbyscore
  CovPlot1 <- coverage_plot(PC, Interactive = NA)
  expect_true(inherits(CovPlot1, "ggplot"))

  # Create an interactive plot with colorbyscore with Score
  CovPlot2 <- coverage_plot(PC, ColorByScore = "Score", Interactive = TRUE)
  expect_true(inherits(CovPlot2, "plotly"))

  # Create a static plot where the requested colorbyscore is NA
  suppressMessages(CovPlot3 <- coverage_plot(PC, "QValue"))
  expect_true(inherits(CovPlot3, "ggplot"))

  # Modify plot coverage to have Q-Values and make an interactive plot
  PC$PeptidesByPosition$`Q Value` <- runif(nrow(PC$PeptidesByPosition))
  CovPlot4 <- coverage_plot(PC, "QValue", TRUE)
  expect_true(inherits(CovPlot4, "plotly"))

})