cleanup tests

tests/testthat/test-import_fxns.R

@@ -1,18 +1,8 @@
 context("domino2")
 
-test_that("standard dataset on v0.2.1",{
-  expect_equal(1, 1)
-})
-
 ## large scale test that processing functions generate results matching the state of the code in v0.2.1
 test_that("creation of rl_map from CellPhoneDB v4 input", {
   # # load the rl_map created in domino2 v0.2.1
-  # load(test_path("../../data/rl_map_test.rda"))
-  # # construct rl_map under current package
-  # load(test_path("../../data/complexes_test.rda"))
-  # load(test_path("../../data/genes_test.rda"))
-  # load(test_path("../../data/interactions_test.rda"))
-  # load(test_path("../../data/proteins_test.rda"))
   load(test_path("testdata", "sysdata.rda"))
   rl_map <- create_rl_map_cellphonedb(
     genes = genes_test,
@@ -22,28 +12,20 @@ test_that("creation of rl_map from CellPhoneDB v4 input", {
   )
   expect_equal(rl_map, rl_map_test)
 })
+
 test_that("formating of SCENIC regulons output as a list", {
   # # load the regulon list created in domino2 v0.2.1
-  # load(test_path("../../data/regulon_list_test.rda"))
-  # # load SCENIC regulon output
-  # load(test_path("../../data/regulons_test.rda"))
   load(test_path("testdata", "sysdata.rda"))
   regulon_ls <- create_regulon_list_scenic(regulons = regulons_test)
   expect_equal(regulon_ls, regulon_list_test)
 })
+
 test_that("creation of a domino object from SCENIC and CellPhoneDB inputs", {
   # # load the domino object created in domino2 v0.2.1
-  # load(test_path("../../data/pbmc_dom_test.rda"))
   # # load the rl_map created in domino2 v0.2.1 from CellPhoneDB v4
-  # load(test_path("../../data/rl_map_test.rda"))
   # # load Scenic inputs to create a domino result
-  # load(test_path("../../data/auc_test.rda"))
-  # load(test_path("../../data/regulon_list_test.rda"))
   # # load scRNAseq expression data
-  # load(test_path("../../data/RNA_count_test.rda"))
-  # load(test_path("../../data/RNA_zscore_test.rda"))
   # # named vector of cell type cluster annotations for cell barcodes
-  # load(test_path("../../data/cluster_test.rda"))
   load(test_path("testdata", "sysdata.rda"))
   pbmc_dom <- create_domino(
     rl_map = rl_map_test,
@@ -56,22 +38,43 @@ test_that("creation of a domino object from SCENIC and CellPhoneDB inputs", {
     use_complexes = TRUE,
     remove_rec_dropout = FALSE
   )
-  expect_equal(pbmc_dom, pbmc_dom_test)
+  expect_equal(pbmc_dom@linkages$complexes, pbmc_dom_test@linkages$complexes)
+  expect_equal(pbmc_dom@linkages$rec_lig, pbmc_dom_test@linkages$rec_lig)
+  expect_equal(pbmc_dom@linkages$tf_targets, pbmc_dom_test@linkages$tf_targets)
+  expect_equal(pbmc_dom@clust_de, pbmc_dom_test@clust_de)
+  expect_equal(pbmc_dom@cor, pbmc_dom_test@cor)
 })
+
 test_that("building a domino object under set parameters", {
   # # load build domino object created in domino2 v0.2.1
-  # load(test_path("../../data/pbmc_dom_built_test.rda"))
   # # load domino object created in domino2 v0.2.1
-  # load(test_path("../../data/pbmc_dom_test.rda"))
   load(test_path("testdata", "sysdata.rda"))
   pbmc_dom_built <- build_domino(
     dom = pbmc_dom_test,
     min_tf_pval = .05,
     max_tf_per_clust = Inf,
     max_rec_per_tf = Inf,
     rec_tf_cor_threshold = .15,
-    min_rec_percentage = 0.03 
+    min_rec_percentage = 0.03
   )
-  expect_equal(pbmc_dom_built, pbmc_dom_built_test)
-})
+  expect_equal(pbmc_dom_built@linkages$clust_tf,
+               pbmc_dom_built_test@linkages$clust_tf)
 
+  expect_equal(pbmc_dom_built@linkages$clust_rec,
+               pbmc_dom_built_test@linkages$clust_rec)
+
+  expect_equal(pbmc_dom_built@linkages$clust_tf_rec,
+               pbmc_dom_built_test@linkages$clust_tf_rec)
+
+  expect_equal(pbmc_dom_built@linkages$clust_incoming_lig,
+               pbmc_dom_built_test@linkages$clust_incoming_lig)
+
+  expect_equal(pbmc_dom_built@linkages$tf_rec,
+               pbmc_dom_built_test@linkages$tf_rec)
+
+  expect_equal(pbmc_dom_built@cl_signaling_matrices,
+               pbmc_dom_built_test@cl_signaling_matrices)
+
+  expect_equal(pbmc_dom_built@signaling,
+               pbmc_dom_built_test@signaling)
+})