tests/testthat/test.add_markers_search.R

In frhl/genoppi-v4: genoppi

context('add_markers_search')

data("example_data")

test_that('basic test to see if function works',{
  
  # perform moderated t-test
  stats_df <- calc_mod_ttest(example_data)
  sig_df <- id_enriched_proteins(stats_df)
  
  # generate volcano plot with bait protein labeled
  basic_volcano <- plot_volcano_basic(sig_df)
  bait_volcano <- plot_overlay(basic_volcano,as.bait('BCL2'))
  
  # interactive volcano plot
  result = make_interactive(bait_volcano) %>%
    add_markers_search('DD')
  
  # check result
  m = result$x$attrs[[5]]
  expect_true(!is.null(m))
  expect_equal(m$hoverinfo, "text+x+y")
  expect_equal(quo_name(m$x), 'logFC')
  expect_equal(quo_name(m$y), "-log10(pvalue)")
  
})

test_that('pathway search',{
  
  # perform moderated t-test
  stats_df <- calc_mod_ttest(example_data)
  sig_df <- id_enriched_proteins(stats_df)
  
  # generate volcano plot with bait protein labeled
  basic_volcano <- plot_volcano_basic(sig_df)
  bait_volcano <- plot_overlay(basic_volcano, as.bait('BCL2'))

  # pathways
  mapping = data.frame(gene=sig_df$gene,pathway='X_PATHWAY',stringsAsFactors = F)
  mapping$pathway[1:5] <- 'Y_PATHWAY'
    
  # interactive volcano plot
  result = make_interactive(bait_volcano) %>%
    add_markers_search_pathway('Y_PATHWAY',mapping)
  
  # chexck result
  m = result$x$attrs[[5]]
  expect_true(!is.null(m))
  expect_equal(m$hoverinfo, "text+x+y")
  expect_equal(quo_name(m$x), 'logFC')
  expect_equal(quo_name(m$y), "-log10(pvalue)")

  
  ## check errors
  
  # if mapping is null return error
  expect_error(add_markers_search_pathway(result, 'Y_PATHWAY',NULL))
  
  # remove ggparams
  result = make_interactive(bait_volcano) 
  result$ggparams <- NULL
  expect_error(add_markers_search(result, 'DD'))
  expect_error(add_markers_search_pathway(result, 'Y_PATHWAY',mapping))
  
})