feat(visualizeNetworks): Enable use of other columns for node labels (#…

…31)

* feat(visualizeNetworks): Enable use of other columns for node labels

R/getSubnetworkFromIndra.R

@@ -25,7 +25,7 @@
 #'     "extdata/groupComparisonModel.csv",
 #'     package = "MSstatsBioNet"
 #' ))
-#' subnetwork <- getSubnetworkFromIndra(input, pvalueCutoff = 0.05)
+#' subnetwork <- getSubnetworkFromIndra(input)
 #' head(subnetwork$nodes)
 #' head(subnetwork$edges)
 #'

R/utils_getSubnetworkFromIndra.R

@@ -9,6 +9,9 @@
     if (nrow(input) >= 400) {
         stop("Invalid Input Error: INDRA query must contain less than 400 proteins.  Consider lowering your p-value cutoff")
     }
+    if (nrow(input) == 0) {
+        stop("Invalid Input Error: Input must contain at least one protein after filtering.")
+    }
 }
 
 #' Call INDRA Cogex API and return response
@@ -189,6 +192,7 @@
         id = input$Protein,
         logFC = input$log2FC,
         pvalue = input$adj.pvalue,
+        hgncName = if ("HgncName" %in% colnames(input) && is.character(input$HgncName)) input$HgncName else NA,
         stringsAsFactors = FALSE
     )
     nodes <- nodes[which(nodes$id %in% edges$source | nodes$id %in% edges$target),]

R/utils_visualizeNetworks.R

@@ -1,8 +1,12 @@
 #' Validate input for MSstatsBioNet visualizeNetworks
 #' @param nodes dataframe of nodes
+#' @param node_label_column column of nodes dataframe for node labeling
 #' @keywords internal
 #' @noRd
-.validateVisualizeNetworks <- function(nodes) {
+.validateVisualizeNetworks <- function(nodes, node_label_column) {
+    if (!node_label_column %in% colnames(nodes)) {
+        stop("The specified node_label_column does not exist in the nodes dataframe.")
+    }
     if (!"logFC" %in% colnames(nodes)) {
         stop("The 'logFC' column is missing from the nodes dataframe.")
     }

R/visualizeNetworks.R

@@ -13,6 +13,8 @@
 #' Default is 0.05
 #' @param logfcCutoff log fold change cutoff for coloring significant
 #' proteins. Default is 0.5
+#' @param node_label_column The column of the nodes dataframe to use as the 
+#' node label.  Default is "id".  "hgncName" can be used for gene name.
 #' @importFrom RCy3 createNetworkFromDataFrames mapVisualProperty
 #' createVisualStyle setVisualStyle layoutNetwork addAnnotationShape
 #' addAnnotationText getNodePosition getNetworkCenter
@@ -32,8 +34,9 @@
 #'
 visualizeNetworks <- function(nodes, edges,
                               pvalueCutoff = 0.05, 
-                              logfcCutoff = 0.5) {
-    .validateVisualizeNetworks(nodes)
+                              logfcCutoff = 0.5,
+                              node_label_column = "id") {
+    .validateVisualizeNetworks(nodes, node_label_column)
 
     # Add additional columns for visualization
     nodes$logFC_color <- nodes$logFC
@@ -55,7 +58,7 @@ visualizeNetworks <- function(nodes, edges,
         VISUAL_STYLE_NAME <- "MSstats-Indra Visual Style"
 
         VISUAL_STYLE_MAPPINGS <- list(
-            mapVisualProperty("Node Label", "id", "p"),
+            mapVisualProperty("Node Label", node_label_column, "p"),
             mapVisualProperty(
                 "Node Fill Color", "logFC_color", "c",
                 c(-logfcCutoff, 0.0, logfcCutoff),