tests/testthat/test-data_convertion.R

In ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

context("Convertion to the graph.")


testdata <- data.frame(competing = c("TP53", "Gene2", "ABCC1", "Gene4", "Gene4", "Gene5", "PTEN"),
                       miRNA = c("mir1", "mir1","hsa-mir3", "mir1", "MiR2", "MiR2", "miR4"),
                       Competing_expression = c(10000, 10000, 5000, 10000, 10000, 5000, 10000),
                       miRNA_expression = c(1000, 1000, 1000, 1000, 2000, 2000, 2000),
                       stringsAsFactors = FALSE)

testdata2 <- data.frame(competing = c("TP53", "Gene-2", "ABCC1", "Gene 4", "Gene 4", "Gene5", "PTEN"),
                        miRNA = c("mir1", "mir1","hsa-mir3", "mir1", "MiR2", "MiR2", "miR4"),
                        Competing_expression = c(10000, 10000, 5000, 10000, 10000, 5000, 10000),
                        miRNA_expression = c(1000, 1000, 1000, 1000, 2000, 2000, 2000),
                        stringsAsFactors = FALSE)

testdata3 <- data.frame(competing = c("TP53", "Gene-2", "ABCC1", "Gene 4", "Gene 4", "Gene5", "PTEN"),
                        miRNA = c("mir1", "mir1","hsa-mir3", "mir1", "MiR2", "MiR2", "miR4"),
                        Competing_expression = c(NA, 10000, 5000, 10000, 10000, 5000, 10000),
                        miRNA_expression = c(1000, 1000, 1000, 1000, 2000, 2000, 2000),
                        stringsAsFactors = FALSE)

test_that("Can dataset be correctly converted to graph ? ", {


 prime_type_1 <-  (priming_graph(testdata, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
                      tidygraph::activate(nodes)%>%
      as_tibble()%>%
      filter(type == "miRNA")%>%
      count())%>%
   pull()

 prime_type_2 <-priming_graph(testdata, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
                   tidygraph::activate(nodes)%>%
     as_tibble()%>%
     filter(type == "Competing")%>%
     count()%>%
   pull()


 prime_type_3 <-  (priming_graph(testdata2, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
                      tidygraph::activate(nodes)%>%
                     as_tibble()%>%
                     filter(type == "miRNA")%>%
                     count())%>%
   pull()

 prime_type_4 <-priming_graph(testdata2, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
    tidygraph::activate(nodes)%>%
   as_tibble()%>%
   filter(type == "Competing")%>%
   count()%>%
   pull()




  expect_equal(prime_type_1 , prime_type_3)
  expect_equal(prime_type_2, prime_type_4)

})


test_that("Is there any missing value that is caused by calculations in graph?", {


  sum(is.na.data.frame(priming_graph(testdata, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
                         as_tibble()))->missings1

  sum(is.na.data.frame(priming_graph(testdata, competing_count = Competing_expression, miRNA_count= miRNA_expression)%>%
                          tidygraph::activate(nodes)%>%
                         as_tibble()))->missings2

  expect_equal(missings1, missings2)


}

)

test_that("When missing value is found in dataframe", {

   expect_warning(priming_graph(testdata3, competing_count = Competing_expression, miRNA_count= miRNA_expression), "Dataframe includes 1 NA values. Dataframe will be processed after NA removing. ")

          }

)

test_that("Simulation on the sample network", {

   data("minsamp")
   data("new_counts")

   minsamp %>%
      priming_graph(competing_count = Competing_expression,
                    miRNA_count = miRNA_expression,
                    aff_factor = c(energy, seed_type),
                    deg_factor = region) %>%
      update_variables(current_counts = new_counts) %>%
      vis_graph()->initialsim_res

   minsamp %>%
      priming_graph(competing_count = Competing_expression,
                    miRNA_count = miRNA_expression,
                    aff_factor = c(energy, seed_type),
                    deg_factor = region) %>%
      update_variables(current_counts = new_counts) %>%
      simulate(3) %>%
      vis_graph(title = "Minsamp Graph After 3 Iteration")->sim_res

   minsamp %>%
      priming_graph(competing_count = Competing_expression,
                    miRNA_count = miRNA_expression,
                    aff_factor = c(energy, seed_type),
                    deg_factor = region) %>%
      update_how("Gene2", how = 3) %>%
      simulate_vis(3, title = "Minsamp Graph After Each Iteration")%>%
      as_tibble()%>%
      filter(count_current == initial_count)%>%
      select(name)%>%
      pull()-> test_sim

   expect_equal(initialsim_res[["data"]][["initial_count"]], initialsim_res[["data"]][["count_pre"]], initialsim_res[["data"]][["count_current"]])
   expect_equal(sim_res[["layers"]][[2]][["aes_params"]][["shape"]], 16)
   expect_equal(test_sim, c("Mir1", "Mir2"))


}

)