tests/testthat/test-plots.R

In scUtils: Utility Functions for Single-Cell RNA Sequencing Data

context("plot functions")



test_that("zero expression is allowed, negative is not", {
  expect_error(feat(data.frame(u1=1:5, u2=5:1), -1:3))
  p <- feat(data.frame(u1=1:5, u2=5:1), 0:4)
  expect_true(min(p$data$expression) > 0)
})

test_that("closed_breaks_log2 output is as expected", {
    expect_equal(closed_breaks_log2(c(.9, 200.1)), c(.9, 4, 16, 64, 200.1))
    expect_equal(closed_breaks_log2(c(.1, 15)), c(.1, .25, 1, 4, 15))
    expect_equal(closed_breaks_log2(c(.1, 500)), c(.1, 1, 8, 64, 500))
    expect_equal(closed_breaks_log2(c(.01, 5000)), c(.01, .25, 8, 256, 5000))
    # falling back to computing mean works (to avoid less than three breaks):
    expect_equal(round(closed_breaks_log2(c(10, 15)),1), c(10, 12.2, 15))
    expect_equal(round(closed_breaks_log2(c(.01, .015)),3), c(.01, .012, .015))
    # zeros throw error; excluding them is not job of the breaks function
    expect_error( closed_breaks_log2(c(0, 4.9)), regexp = "finite number" )
})




test_that("closed_labels output is as expected",{
  expect_equal( closed_labels(c(.9, 2, 8, 32, 200.1)), c(".9", "2", "8", "32", "200.1") )
  expect_equal(closed_labels(c(.1, .25, 1, 4, 15)), c(".1", ".25", "1", "4", "15"))
  expect_equal(closed_labels(c(.1, .5, 4, 32, 500)), c(".1", ".5", "4", "32", "500") )
  expect_equal(closed_labels(c(.12444, .5, 4, 32, 256, 977.223)),
               c(".12", ".5", "4", "32", "256", "977.2"))
  # note that .125 is rounded to .12 on Linux. On OS, this might be different.
  expect_equal( closed_labels(c(.038, .125, .5, 2, 14.8)), c(".04", ".12", ".5", "2", "14.8") )
  expect_equal( closed_labels(c(426, 10000, 161333)), c("426", "1e+04", "1.6e+05") )
})






test_that("all kinds of colnames are allowed", {
  # u1/2 and something that is not u1/2
  p <- feat(data.frame(u1=rnorm(150, c(1, 8)), u2=rnorm(150, c(-1, 1))),
       expression = rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p))
  p <- feat(data.frame(d1=rnorm(150, c(1, 8)), d2=rnorm(150, c(-1, 1))),
       expression = rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p))
  # special characters in dim names
  p <- feat(data.frame(p_1_2=rnorm(150, c(1, 8)), b..2=rnorm(150, c(-1, 1))),
       expression = rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p))
  # colnames are NULL
  df <- data.frame(p_1_2=rnorm(150, c(1, 8)), b..2=rnorm(150, c(-1, 1)))
  colnames(df) <- NULL
  p <- feat(df, expression = rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p))
  expect_equal(p$labels, list(y="Dim2", x="Dim1", colour="expression"))
})


test_that("All kinds of 2D embeddings are allowed", {
  # matrix is allowed
  p<-feat(matrix(c(rnorm(150, c(1,8)), rnorm(150, c(-1,1))), ncol=2,
                dimnames = list(as.character(1:150), c("m1", "m2"))),
       expression =rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p)); rm(p)
  # matrix with empty dimnames:
  p <- feat(matrix(c(rnorm(150, c(1,8)), rnorm(150, c(-1,1))), ncol=2,
                dimnames = list(NULL)),
       expression =rlnorm(150, meanlog=c(0, 3)))
  expect_silent(print(p)); rm(p)
  # tibble is allowed
  if(requireNamespace("tibble", quietly = TRUE)) {
   p <- feat(tibble::tibble(d1=rnorm(150, c(1, 8)), d2=rnorm(150, c(-1, 1))),
       expression = rlnorm(150, meanlog=c(0, 3)))
   expect_silent(print(p)); rm(p)
  }

})