Moved {networkD3} to Suggests

almeidasilvaf · Oct 8, 2024 · bcffc9a · bcffc9a
1 parent 2b17e15
commit bcffc9a
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Showing 4 changed files with 12 additions and 8 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -304,7 +304,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results
           path: check

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -48,7 +48,7 @@ biocViews: Software,
     Network
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
     Rcpp (>= 1.0.8),
     BiocParallel,
@@ -65,8 +65,7 @@ Imports:
     pheatmap,
     ggplot2,
     ggnetwork,
-    intergraph,
-    networkD3
+    intergraph
 Suggests:
     BiocStyle,
     ggtree,
@@ -75,7 +74,8 @@ Suggests:
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),
-    xml2
+    xml2,
+    networkD3
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 LinkingTo:

diff --git a/NAMESPACE b/NAMESPACE
@@ -52,8 +52,6 @@ importFrom(igraph,cluster_infomap)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,simplify)
 importFrom(methods,is)
-importFrom(networkD3,forceNetwork)
-importFrom(networkD3,igraph_to_networkD3)
 importFrom(pheatmap,pheatmap)
 importFrom(rlang,.data)
 importFrom(rtracklayer,import)

diff --git a/R/06_dataviz.R b/R/06_dataviz.R
@@ -176,7 +176,6 @@ plot_profiles <- function(
 #' @return A ggplot object with the network.
 #' 
 #' @importFrom ggnetwork ggnetwork theme_blank geom_edges geom_nodes
-#' @importFrom networkD3 igraph_to_networkD3 forceNetwork
 #' @importFrom igraph graph_from_data_frame
 #' @importFrom ggplot2 aes ggplot scale_color_manual guides
 #' @importFrom grDevices colorRampPalette
@@ -241,6 +240,12 @@ plot_network <- function(network = NULL, clusters = NULL,
         palette <- colorRampPalette(custom_palette(1))(nlevels(genes$Group))
     }
     if(interactive) {
+        if(!requireNamespace("networkD3", quietly = TRUE)) {
+            stop(
+                "Package 'networkD3' is required for interactive visualizations.\n",
+                "You can install it with `BiocManager::install('networkD3')`."
+            )
+        }
         graph_d3 <- networkD3::igraph_to_networkD3(graph, group = genes)
         d <- dim_interactive
         p <- networkD3::forceNetwork(
@@ -250,6 +255,7 @@ plot_network <- function(network = NULL, clusters = NULL,
             height = d[2], width = d[1], Nodesize = 'Degree',
             opacity=0.8, zoom = TRUE, fontSize = 12
         )
+
     } else {
         n <- ggnetwork::ggnetwork(graph, arrow.gap = 0)
         # Plot graph