refactor(visualize): Change name of function visualizeSubnetwork to v…

…isualizeNetworks
Vitek-Lab · Jul 25, 2024 · 31b9227 · 31b9227
1 parent 929df93
commit 31b9227
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Showing 5 changed files with 23 additions and 23 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,7 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(getSubnetworkFromIndra)
-export(visualizeSubnetwork)
+export(visualizeNetworks)
 importFrom(RCy3,createNetworkFromDataFrames)
 importFrom(RCy3,createVisualStyle)
 importFrom(RCy3,mapVisualProperty)

diff --git a/R/visualizeSubnetwork.R → R/visualizeNetworks.R b/R/visualizeSubnetwork.R → R/visualizeNetworks.R
@@ -17,13 +17,13 @@
 #'     package = "MSstatsBioNet"
 #' ))
 #' # subnetwork = getSubnetworkFromIndra(input)
-#' # visualizeSubnetwork(subnetwork$nodes, subnetwork$edges)
+#' # visualizeNetworks(subnetwork$nodes, subnetwork$edges)
 #'
 #' @return cytoscape visualization of subnetwork
 #'
 #'
-visualizeSubnetwork <- function(nodes, edges,
-                                pvalue_cutoff = 0.05, logfc_cutoff = 0.5) {
+visualizeNetworks <- function(nodes, edges,
+                              pvalue_cutoff = 0.05, logfc_cutoff = 0.5) {
     # Add additional columns for visualization
     nodes$logFC_color <- nodes$logFC
     nodes$logFC_color[nodes$pvalue > pvalue_cutoff |

diff --git a/man/visualizeSubnetwork.Rd → man/visualizeNetworks.Rd b/man/visualizeSubnetwork.Rd → man/visualizeNetworks.Rd
diff --git a/tests/testthat/test-visualizeSubnetwork.R → tests/testthat/test-visualizeNetworks.R b/tests/testthat/test-visualizeSubnetwork.R → tests/testthat/test-visualizeNetworks.R
@@ -1,64 +1,64 @@
-test_that("visualizeSubnetwork works correctly", {
+test_that("visualizeNetworks works correctly", {
     input <- readRDS(system.file("processed_data/subnetwork.rds",
         package = "MSstatsBioNet"
     ))
 
     mock_createNetworkFromDataFrames <- mock()
     stub(
-        visualizeSubnetwork, "createNetworkFromDataFrames",
+        visualizeNetworks, "createNetworkFromDataFrames",
         mock_createNetworkFromDataFrames
     )
     mock_mapVisualProperty <- mock()
     stub(
-        visualizeSubnetwork, "mapVisualProperty",
+        visualizeNetworks, "mapVisualProperty",
         mock_mapVisualProperty
     )
     mock_createVisualStyle <- mock()
     stub(
-        visualizeSubnetwork, "createVisualStyle",
+        visualizeNetworks, "createVisualStyle",
         mock_createVisualStyle
     )
     mock_setVisualStyle <- mock()
     stub(
-        visualizeSubnetwork, "setVisualStyle",
+        visualizeNetworks, "setVisualStyle",
         mock_setVisualStyle
     )
 
-    expect_silent(visualizeSubnetwork(input$nodes, input$edges))
+    expect_silent(visualizeNetworks(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", {
+test_that("visualizeNetworks with p-value and logFC constraints works", {
     input <- readRDS(system.file("processed_data/subnetwork.rds",
         package = "MSstatsBioNet"
     ))
 
     mock_createNetworkFromDataFrames <- mock()
     stub(
-        visualizeSubnetwork, "createNetworkFromDataFrames",
+        visualizeNetworks, "createNetworkFromDataFrames",
         mock_createNetworkFromDataFrames
     )
     mock_mapVisualProperty <- mock()
     stub(
-        visualizeSubnetwork, "mapVisualProperty",
+        visualizeNetworks, "mapVisualProperty",
         mock_mapVisualProperty
     )
     mock_createVisualStyle <- mock()
     stub(
-        visualizeSubnetwork, "createVisualStyle",
+        visualizeNetworks, "createVisualStyle",
         mock_createVisualStyle
     )
     mock_setVisualStyle <- mock()
     stub(
-        visualizeSubnetwork, "setVisualStyle",
+        visualizeNetworks, "setVisualStyle",
         mock_setVisualStyle
     )
 
-    expect_silent(visualizeSubnetwork(input$nodes, input$edges,
+    expect_silent(visualizeNetworks(input$nodes, input$edges,
         pvalue_cutoff = 0.01, logfc_cutoff = 2.5
     ))
     expect_called(mock_createNetworkFromDataFrames, 1)

diff --git a/vignettes/MSstatsBioNet.Rmd b/vignettes/MSstatsBioNet.Rmd
@@ -28,7 +28,7 @@ networks. The package is designed to be used in conjunction with the
 
 The package provides a function `getSubnetworkFromIndra` that retrieves a
 subnetwork of proteins from the INDRA database based on differential abundance
-analysis results.  The function `visualizeSubnetwork` then takes the output
+analysis results.  The function `visualizeNetworks` then takes the output
 of `getSubnetworkFromIndra` and visualizes the subnetwork.
 
 ```{r proteinNetworkDiscovery, eval=FALSE}
@@ -38,5 +38,5 @@ input <- data.table::fread(
     )
 )
 subnetwork <- getSubnetworkFromIndra(input)
-visualizeSubnetwork(subnetwork$nodes, subnetwork$edges)
+visualizeNetworks(subnetwork$nodes, subnetwork$edges)
 ```