fix unit tests

Vitek-Lab · Jan 10, 2025 · 8dd0029 · 8dd0029
1 parent 06308c5
commit 8dd0029
Show file tree

Hide file tree

Showing 3 changed files with 31 additions and 20 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -7,7 +7,6 @@ importFrom(RCy3,addAnnotationShape)
 importFrom(RCy3,addAnnotationText)
 importFrom(RCy3,createNetworkFromDataFrames)
 importFrom(RCy3,createVisualStyle)
-importFrom(RCy3,getAnnotationList)
 importFrom(RCy3,getNetworkCenter)
 importFrom(RCy3,getNodePosition)
 importFrom(RCy3,groupAnnotation)

diff --git a/R/utils_visualizeNetworks.R b/R/utils_visualizeNetworks.R
@@ -1,25 +1,40 @@
 #' Add a legend using annotations
 #' @param legend_items list of items and properties
 #' @importFrom RCy3 addAnnotationShape addAnnotationText getNodePosition 
-#' getNetworkCenter groupAnnotation getAnnotationList
+#' getNetworkCenter groupAnnotation
 #' @keywords internal
 #' @noRd
 .addLegendInCytoscape <- function(legend_items) {
     # Starting position for the legend
-    node_coordinates = getNodePosition()
-    node_coordinates$x_location = as.numeric(node_coordinates$x_location)
+    node_coordinates <- getNodePosition()
+    node_coordinates$x_location <- as.numeric(node_coordinates$x_location)
     x_start <- max(node_coordinates$x_location) + 50  # Place the legend 50 units to the right of the rightmost node
     y_start <-  getNetworkCenter()$y
     box_size <- 20 # Size of the color boxes
     spacing <- 10  # Spacing between legend items
+    legend_title <- "Legend"
+    title_spacing <- 20  # Additional spacing below the title
+    annotation_names <- c()
+
+    title_name <- addAnnotationText(
+        text = legend_title,
+        x.pos = x_start, # Center the title with respect to the legend
+        y.pos = y_start,  # Position above the items
+        fontSize = 14,
+        color = "black"
+    )
+    annotation_names <- c(annotation_names, title_name)
+
+    # Adjust the starting y-coordinate for the legend items
+    y_start <- y_start + title_spacing
 
     # Loop to add shapes and text for each legend item
     for (i in seq_along(legend_items)) {
         item <- legend_items[[i]]
-        y_pos <- y_start - (i - 1) * (box_size + spacing)  # Adjust position for each item
+        y_pos <- y_start + (i - 1) * (box_size + spacing)  # Adjust position for each item
 
         # Add a colored rectangle for the legend
-        addAnnotationShape(
+        shape_name <- addAnnotationShape(
             type = "rectangle",
             x.pos = x_start,
             y.pos = y_pos,
@@ -31,14 +46,18 @@
         )
 
         # Add corresponding text label
-        addAnnotationText(
+        text_name <- addAnnotationText(
             text = item$label,
             x.pos = x_start + box_size + spacing,
-            y.pos = y_pos + box_size / 2,  # Center text vertically with the rectangle
+            y.pos = y_pos + box_size / 4,  # Center text vertically with the rectangle
             fontSize = 12,
             color = "black"
         )
+
+        annotation_names <- c(annotation_names, shape_name, text_name)
     }
     # Group all annotations for now
-    groupAnnotation(sapply(getAnnotationList(), '[[', 'uuid'))
+    groupAnnotation(
+        names = annotation_names
+    )
 }
diff --git a/tests/testthat/test-utils_visualizeNetworks.R b/tests/testthat/test-utils_visualizeNetworks.R
@@ -5,7 +5,7 @@ test_that(".addLegendInCytoscape works correctly", {
         list(color = "#FFA590", label = "label3")
     )
 
-    mock_getNodePosition <- mock(data.frame(x_position = c("50", "51")))
+    mock_getNodePosition <- mock(data.frame(x_location = c("50", "51")))
     stub(
         .addLegendInCytoscape, "getNodePosition",
         mock_getNodePosition
@@ -17,13 +17,13 @@ test_that(".addLegendInCytoscape works correctly", {
         mock_getNetworkCenter
     )
 
-    mock_addAnnotationShape <- mock()
+    mock_addAnnotationShape <- mock("id-12345", cycle = TRUE)
     stub(
         .addLegendInCytoscape, "addAnnotationShape",
         mock_addAnnotationShape
     )
 
-    mock_addAnnotationText <- mock()
+    mock_addAnnotationText <- mock("id-12345", cycle = TRUE)
     stub(
         .addLegendInCytoscape, "addAnnotationText",
         mock_addAnnotationText
@@ -35,17 +35,10 @@ test_that(".addLegendInCytoscape works correctly", {
         mock_groupAnnotation
     )
 
-    mock_getAnnotationList <- mock(c("id1", "id2"))
-    stub(
-        .addLegendInCytoscape, "getAnnotationList",
-        mock_getAnnotationList
-    )
-
     expect_silent(.addLegendInCytoscape(legend_items))
     expect_called(mock_getNodePosition, 1)
     expect_called(mock_getNetworkCenter, 1)
     expect_called(mock_addAnnotationShape, 3)
-    expect_called(mock_addAnnotationText, 3)
+    expect_called(mock_addAnnotationText, 4)
     expect_called(mock_groupAnnotation, 1)
-    expect_called(mock_getAnnotationList, 1)
 })