improve unit tests

NAMESPACE

@@ -48,6 +48,7 @@ export(rawMap)
 export(rawValue)
 export(return_line_compounds)
 import(BiocFileCache)
+import(Cairo)
 import(ggplot2)
 import(ggraph)
 import(igraph)

R/ggkegg.R

@@ -40,6 +40,7 @@
 #' g + geom_node_rect()
 #' @import ggraph
 #' @import ggplot2
+#' @import Cairo
 #' @importFrom tidygraph as_tbl_graph
 #' @importFrom igraph induced.subgraph delete_vertex_attr
 #' @importFrom methods new

tests/testthat/test-highlight.R

@@ -1,9 +1,18 @@
-test_that("Highlight functions without errors", {
+test_that("Highlight node functions without errors", {
 	graph <- create_test_pathway()
-	expect_error( graph |> mutate(hl=highlight_set_nodes(c("hsa:51428"))), NA)
-	expect_error( graph |> activate("edges") |>
+	expect_error(graph |> mutate(hl=highlight_set_nodes(c("hsa:51428"))), NA)
+})
+test_that("Highlight edge functions without errors", {
+	graph <- create_test_pathway()
+	expect_error(graph |> activate("edges") |>
         mutate(hl=highlight_set_edges(c("degradation"),
             name="subtype_name")), NA)
 })
+test_that("Highlight module functions without errors", {
+	graph <- create_test_pathway()
+    mo <- create_test_module()
+	expect_error(graph <- graph |> highlight_module(mo), NA)
+})
+
 
 

tests/testthat/test-module.R

@@ -1,9 +1,15 @@
-test_that("Module parsing without errors", {
+test_that("Module parsing to text and network without errors", {
 	expect_error( create_test_module(), NA)
 	mod <- create_test_module()
+
+	## Text parsing
 	expect_error( module_text(mod), NA)
 	expect_error( module_text(mod) |> plot_module_text(), NA)
     mod <- module("M00004")
     expect_error( module_text(mod), NA)
     expect_error( module_text(mod) |> plot_module_text(), NA)
+
+    ## Network parsing
+    expect_error( obtain_sequential_module_definition(mod) |>
+        plot_module_blocks(), NA)
 })

tests/testthat/test-pathway.R

@@ -1,3 +1,12 @@
-test_that("Pathway parsing without errors", {
+test_that("Generate test pathway without errors", {
 	expect_error( create_test_pathway(), NA)
 })
+test_that("Pathway downloading without errors", {
+	expect_error( pathway("hsa04110"), NA)
+})
+test_that("process_line without errors", {
+	expect_error( create_test_pathway(line=TRUE) |> process_line(), NA)
+})
+test_that("process_reaction without errors", {
+	expect_error( create_test_pathway(line=TRUE) |> process_reaction(), NA)
+})

tests/testthat/test-utils.R

@@ -10,3 +10,14 @@ test_that("Do utils without errors", {
                                     name="graphics_name")),
         NA)
 })
+
+test_that("edge_matrix without errors", {
+	graph <- create_test_pathway()
+    num_df <- data.frame(row.names=c("6737","51428"),
+                    "sample1"=c(1.1,1.2),
+                    "sample2"=c(1.1,1.2),
+                     check.names=FALSE)
+    expect_error(graph <- graph |> edge_matrix(num_df, gene_type="ENTREZID"),
+    	NA)                     	
+})
+