tests/testthat/test-ggcyto-gs.R

In ggcyto: Visualize Cytometry data with ggplot

context("ggcyto-GatingSet")

# options(warn = -1)#suppress removing rows warnings from ggplot

set.seed(1)#due to subsampling
gs_dir1 <- list.files(dataDir, pattern = "gs_manual",full = TRUE)
gs1 <- load_gs(gs_dir1)
if(get_default_backend()=="tile")
{
  tmp <- tempfile()
  convert_backend(gs_dir1, tmp)
  gs_dir1 <- tmp
}
gs1 <- load_gs(gs_dir1)

teardown({
  if(get_default_backend()=="tile")
  {
    message("clean up ", gs_dir1)
    unlink(gs_dir1)
  }
})


test_that("gs", {
  

  p <- ggcyto(gs1, aes(x = CD4, y = CD8), subset = "CD3+")
  # 2d plot
  p <- p + geom_hex(bins = 64)
  suppressWarnings(expect_doppelganger("ggcyto-gs-2d", p))

  suppressWarnings(expect_doppelganger("ggcyto-gs-instrument-range", p + ggcyto_par_set(limits = "instrument")))

  myPars <- ggcyto_par_set(limits = list(x = c(0,3.5e3), y = c(-10, 4.1e3)))
  p <- p + myPars# or xlim(0,3.5e3) + ylim(-10, 4e3)
  suppressWarnings(expect_doppelganger("ggcyto-gs-custom-range", p))

  expect_is(ggcyto_par_default(), "ggcyto_par")

  suppressWarnings(expect_doppelganger("ggcyto-gs-1-gate", p + geom_gate("CD4")))


  p <- p + geom_gate(c("CD4","CD8")) # short for geom_gate("CD8") + geom_gate("CD4")
  suppressWarnings(expect_doppelganger("ggcyto-gs-2-gate", p))

  suppressWarnings(expect_doppelganger("ggcyto-gs-stats-all", p + geom_stats() + labs_cyto("marker")))

  suppressWarnings(expect_doppelganger("ggcyto-gs-stats", p + geom_stats("CD4")))


  suppressWarnings(expect_doppelganger("ggcyto-gs-stats-custom", p + geom_stats("CD4", type = "count", size = 6,  color = "white", fill = "black", adjust = 0.3)))


  p <- ggcyto(gs1, aes(x = CD4, y = CD8)) + geom_hex() + myPars
  expect_error(plot(p), "'subset' must be instantiated")

  ## ------------------------------------------------------------------------
  p <- p + geom_gate(c("CD4", "CD8"))


  suppressWarnings(expect_doppelganger("ggcyto-gs-overlay-2d", p + geom_overlay("CD8/CCR7- 45RA+", col = "black", size = 0.1, alpha = 0.4)))

  p <- ggcyto(gs1, aes(x = CD4), subset = "CD3+") + geom_density(aes(y = ..count..))
  suppressWarnings(expect_doppelganger("ggcyto-gs-overlay-1d", p + geom_overlay("CD8/CCR7- 45RA+", aes(y = ..count..), fill = "red")))

  ## ------------------------------------------------------------------------
  p <- ggcyto(gs1, aes(x = 38, y = DR), subset = "CD4") + geom_hex(bins = 64) + geom_gate() + geom_stats()
  suppressWarnings(expect_doppelganger("ggcyto-gs-all-children", p))

  suppressWarnings(expect_doppelganger("ggcyto-gs-root", ggcyto(gs1, subset = "root", aes(x = CD4, y = CD8)) + geom_hex(bins = 64) + geom_gate("CD4") + myPars))


  suppressWarnings(expect_doppelganger("ggcyto-gs-axis_x_inverse_trans", p + axis_x_inverse_trans() + axis_y_inverse_trans()))


})

test_that("stats_null", {
  
  p <- autoplot(gs1, "CD4")
  p <- p + stats_null()
  suppressWarnings(expect_doppelganger("stats_null_1gate", p))
  p <- p + geom_stats(type = "count")
  suppressWarnings(expect_doppelganger("stats_null_1gate_geom_stats", p))
  
  p <- autoplot(gs1, c("CD4", "CD8"))
  p <- p + stats_null()
  suppressWarnings(expect_doppelganger("stats_null_2gates", p))
  p <- p + geom_stats()
  suppressWarnings(expect_doppelganger("stats_null_2gates_geom_stats", p))
  
})

test_that("gate_null", {
  
  p <- autoplot(gs1, c("CD4", "CD8"))
  p <- p + gate_null()
  suppressWarnings(expect_doppelganger("gate_null_2gates", p))
  p <- p + geom_gate("CD4")
  suppressWarnings(expect_doppelganger("gate_null_2gates_geom_gate", p))
  
})
# options(warn = 0)#restore default