tests/testthat/test-add_pathways.R

In MSKCC-Epi-Bio/gnomeR: Wrangle and analyze IMPACT and TCGA mutation data

# Ideas for tests to be added-----------
#
# Test that if custom_pathway with no suffix passed it will error e.g. c(TP53, APC)
test_that("vector custom pathway no suffix with NULL pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  expect_error(add_pathways(gene_binary = gene_binary_ex,
                            pathways = NULL,
                            custom_pathways = c("TP53", "APC")), "All alterations*")
})

# Test the above when list or vector passed to custom_pathway
# example of list
# custom_pathways = list(
#   c("TP53.any", "APC"),
#   c("RB1.Del", "FGFR3.any"))
test_that("vector custom pathway no suffix list with NULL pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  expect_error(add_pathways(gene_binary = gene_binary_ex,
                            pathways = NULL,
                            custom_pathways = list(
                                 c("TP53.any", "APC"),
                                 c("RB1.Del", "FGFR3.any"))), "All alterations*")
})

# Test that .any works and .all does not
test_that("pass .any custom pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  expect_error(p <- add_pathways(gene_binary = gene_binary_ex,
                                 pathways = NULL, custom_pathways = c("TP53.any")), NA)

  expect_equal(c(names(gene_binary_ex), "pathway_custom"), names(p))

  expect_error(p <- add_pathways(gene_binary = gene_binary_ex,
                                 pathways = NULL, custom_pathways=c("TP53.all")),"All alterations*")

})


# Test that passing custom pathway with GENE.any would return same as
# custom pathway with GENE.mut, GENE.Del, GENE.Amp, GENE.fus

test_that("vector custom pathway with .any with NULL pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  cust <- add_pathways(gene_binary = gene_binary_ex,
                       pathways = NULL,
                       custom_pathways = c("TP53.any"))

  cust1 <- add_pathways(gene_binary = gene_binary_ex,
                       pathways = NULL,
                       custom_pathways = c("TP53.mut", "TP53.Del", "TP53.Amp", "TP53.fus"))

  expect_equal(names(cust), names(cust1))
  expect_equal(cust$pathway_custom, cust1$pathway_custom)


})

#
# Test that a binary matrix with columns that have .mut suffix (e.g. column name TP53.mut) will correctly be
# processed same as columns with no suffix  (e.g. column name TP53)
#
test_that("test TP53.mut and TP53 are processed the same way", {

  binmat <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10,],
                                       cna = gnomeR::cna,
                                       fusion = gnomeR::sv[1:10,])
  binmat1 = binmat %>%
    select(sample_id, PARP1, AKT1, EGFR.Amp)

  binmat2 = binmat %>%
    select(sample_id, PARP1, AKT1, EGFR.Amp)%>%
    rename(PARP1.mut = PARP1,
           AKT1.mut = AKT1)

  cust1 <- add_pathways(gene_binary = binmat1,
                       pathways = NULL,
                       custom_pathways = c("PARP.mut", "AKT1.mut", "EGFR.Amp"))

  cust2 <- add_pathways(gene_binary = binmat2,
                        pathways = NULL,
                        custom_pathways = c("PARP.mut", "AKT1.mut", "EGFR.Amp")) %>%
    rename_with(., ~str_remove_all(.x, ".mut"), contains(".mut"),)


  expect_equal(cust1, cust2)

  path1 <- add_pathways(gene_binary = binmat1,
                        custom_pathways = c("PARP.mut", "AKT1.mut"))

  path2 <- add_pathways(gene_binary = binmat2,
                        custom_pathways = c("PARP.mut", "AKT1.mut")) %>%
    rename_with(., ~str_remove_all(.x, ".mut"), contains(".mut"),)


  expect_equal(path1, path2)


})


# Make sure all works with both a few default `pathways` AND `custom_pathways` passed at the same time

test_that("add_pathways function works with default input", {

  binmat <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10,],
                                  cna = gnomeR::cna,
                                  fusion = gnomeR::sv[1:10,])

  expect_error(p <- add_pathways(gene_binary = binmat), NA)
  expect_equal(setdiff(names(p), names(binmat)), paste0("pathway_", names(gnomeR::pathways)))


})


test_that("function can be piped from create_gene_binary()", {

  expect_error(gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                     cna = gnomeR::cna,
                                     fusion = gnomeR::sv[1:10,]) %>%
                 add_pathways(), NA)
})

# # pathways -------------------------------------------------------------
test_that("pass specific pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                          cna = gnomeR::cna,
                                          fusion = gnomeR::sv[1:10,])

  expect_error(p <- add_pathways(gene_binary = gene_binary_ex,
                                      pathways = c("Notch")), NA)

  expect_equal(c(names(gene_binary_ex), "pathway_Notch"), names(p))

  expect_error(p <- add_pathways(gene_binary = gene_binary_ex,
                                 pathways = c("Notch", "Myc")), NA)

  expect_warning(p <- add_pathways(gene_binary = gene_binary_ex,
                                 pathways = c("Notch", "no")), "Ignoring*")

  expect_equal(c(names(gene_binary_ex), "pathway_Notch"), names(p))

})


test_that("vector custom pathway with NULL pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  cust <- add_pathways(gene_binary = gene_binary_ex,
                                      pathways = NULL,
                                      custom_pathways = c("TP53.mut", "APC.Del"))

  expect_equal(c(names(gene_binary_ex), "pathway_custom"),
               names(cust))
})

test_that("list custom pathway with NULL pathways", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  cust <- add_pathways(gene_binary = gene_binary_ex,
                                      pathways = NULL,
                                      custom_pathways = list(
                                        "paththingyyy" = c("TP53.mut", "APC.mut"),
                                        "patheroo" = c("RB1.Del")))

  expect_equal(c(names(gene_binary_ex), "pathway_paththingyyy", "pathway_patheroo"),
               names(cust))
})

test_that("list custom pathway with NULL names", {


  gene_binary_ex <- gnomeR::create_gene_binary(mutation = gnomeR::mutations[1:10, ],
                                               cna = gnomeR::cna,
                                               fusion = gnomeR::sv[1:10,])

  cust <- add_pathways(gene_binary = gene_binary_ex,
                                      pathways = NULL,
                                      custom_pathways = list(
                                        c("TP53.mut", "APC.mut"),
                                        c("RB1.Del")))


  expect_equal(c(names(gene_binary_ex), "pathway_custom_1", "pathway_custom_2"),
               names(cust))

})

test_that("check bug with custom pathways not counting .all", {

  tdf <- tibble::tribble(
    ~sample_id,             ~CDKN2A.fus, ~CDKN2A.Del, ~CDKN2B.fus, ~CDKN2B.Del,
    "P-0044370-T01-IM6",           1,           0,           0,           0,
    "P-0050457-T01-IM6",           0,           0,           0,           0,
    "P-0001517-T01-IM3",           1,           0,           0,           0,
    "P-0013235-T01-IM5",           0,           1,           0,           1,
    "P-0015145-T01-IM6",           1,           1,           0,           1,
    "P-0031480-T01-IM6",           0,           0,           0,           0,
    "P-0001461-T01-IM3",           0,           0,           0,           0,
    "P-0015041-T01-IM6",           0,           1,           0,           1,
    "P-0002293-T01-IM3",           0,           1,           0,           1,
    "P-0007501-T01-IM5",           0,           0,           0,           0,
    "P-0029150-T01-IM6",           0,           0,           0,           0,
    "P-0007976-T01-IM5",           0,           1,           0,           1,
    "P-0012178-T01-IM5",           0,           0,           1,           0,
    "P-0003927-T01-IM3",           0,           0,           0,           0,
    "P-0049934-T01-IM6",           0,           0,           0,           0,
    "P-0020389-T01-IM6",           0,           1,           0,           1,
    "P-0025934-T01-IM6",           0,           0,           0,           0,
    "P-0020162-T01-IM6",           0,           0,           0,           0,
    "P-0006901-T01-IM5",           0,           0,           0,           0,
    "P-0031004-T01-IM6",           0,           0,           0,           0
  )

  g <- tdf %>%
    add_pathways(pathways = NULL, custom_pathways = c("CDKN2A.any", "CDKN2B.any")) %>%
    tbl_genomic()

  expect_equal(sum(apply(select(tdf, -sample_id), 1,  sum) > 0), 9)

}




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