test(visualizeSubnetwork): Add unit tests for visualizeSubnetwork

DESCRIPTION

@@ -26,7 +26,8 @@ Suggests:
     BiocStyle,
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    mockery
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, 
     QualityControl

inst/processed_data/groupComparisonModel.csv

@@ -1,5 +1,5 @@
 ,Protein,Label,log2FC,SE,Tvalue,DF,pvalue,adj.pvalue,issue,MissingPercentage,ImputationPercentage,HgncId
-1,BRD2_HUMAN,DMSO-DbET6,2.046185244,0.114338622,17.89583616,260,0,0,NA,0.310067114,0,1103
-2,BRD3_HUMAN,DMSO-DbET6,3.333427936,0.126570545,26.33652185,257,0,0,NA,0.252348993,0,1104
-3,BRD4_HUMAN,DMSO-DbET6,2.668934662,0.101282782,26.35131665,257,0,0,NA,0.118120805,0,13575
+1,BRD2_HUMAN,DMSO-DbET6,2.046185244,0.114338622,17.89583616,260,0,0.001,NA,0.310067114,0,1103
+2,BRD3_HUMAN,DMSO-DbET6,3.333427936,0.126570545,26.33652185,257,0,0.001,NA,0.252348993,0,1104
+3,BRD4_HUMAN,DMSO-DbET6,2.668934662,0.101282782,26.35131665,257,0,0.04,NA,0.118120805,0,13575
 4,CLH1_HUMAN,DMSO-DbET7,0.668934662,0.101282782,2.35131665,257,0.99,0.99,NA,0.118120805,0,2092

tests/testthat.R

@@ -7,6 +7,7 @@
 # * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
+library(mockery)
 library(MSstatsBioNet)
 
 test_check("MSstatsBioNet")

tests/testthat/test-visualizeSubnetwork.R

@@ -0,0 +1,74 @@
+test_that("visualizeSubnetwork works correctly", {
+    input <- readRDS(system.file("processed_data/subnetwork.rds",
+        package = "MSstatsBioNet"
+    ))
+
+    mock_createNetworkFromDataFrames <- mock()
+    stub(
+        visualizeSubnetwork, "createNetworkFromDataFrames",
+        mock_createNetworkFromDataFrames
+    )
+    mock_mapVisualProperty <- mock()
+    stub(
+        visualizeSubnetwork, "mapVisualProperty",
+        mock_mapVisualProperty
+    )
+    mock_createVisualStyle <- mock()
+    stub(
+        visualizeSubnetwork, "createVisualStyle",
+        mock_createVisualStyle
+    )
+    mock_setVisualStyle <- mock()
+    stub(
+        visualizeSubnetwork, "setVisualStyle",
+        mock_setVisualStyle
+    )
+
+    expect_silent(visualizeSubnetwork(input$nodes, input$edges))
+    expect_called(mock_createNetworkFromDataFrames, 1)
+    expect_called(mock_mapVisualProperty, 2)
+    expect_called(mock_createVisualStyle, 1)
+    expect_called(mock_setVisualStyle, 1)
+})
+
+
+test_that("visualizeSubnetwork with p-value and logFC constraints works", {
+    input <- readRDS(system.file("processed_data/subnetwork.rds",
+        package = "MSstatsBioNet"
+    ))
+
+    mock_createNetworkFromDataFrames <- mock()
+    stub(
+        visualizeSubnetwork, "createNetworkFromDataFrames",
+        mock_createNetworkFromDataFrames
+    )
+    mock_mapVisualProperty <- mock()
+    stub(
+        visualizeSubnetwork, "mapVisualProperty",
+        mock_mapVisualProperty
+    )
+    mock_createVisualStyle <- mock()
+    stub(
+        visualizeSubnetwork, "createVisualStyle",
+        mock_createVisualStyle
+    )
+    mock_setVisualStyle <- mock()
+    stub(
+        visualizeSubnetwork, "setVisualStyle",
+        mock_setVisualStyle
+    )
+
+    expect_silent(visualizeSubnetwork(input$nodes, input$edges,
+        pvalue_cutoff = 0.01, logfc_cutoff = 2.5
+    ))
+    expect_called(mock_createNetworkFromDataFrames, 1)
+    calls <- mock_args(mock_createNetworkFromDataFrames)
+    nodes <- calls[[1]][[1]]
+    edges <- calls[[1]][[2]]
+    expect_equal(edges, input$edges)
+    expect_equal(nodes[input$nodes$id == "BRD2_HUMAN", ]$logFC_color, 0)
+    expect_equal(
+        nodes[input$nodes$id == "BRD3_HUMAN", ]$logFC_color, 3.33342794
+    )
+    expect_equal(nodes[input$nodes$id == "BRD4_HUMAN", ]$logFC_color, 0)
+})