Merge branch 'main' into layouts

NAMESPACE

@@ -16,11 +16,9 @@ export(KPartiteNetwork)
 export(Link)
 export(LinkList)
 export(Network)
-export(Node)
 export(NodeId)
 export(NodeIdList)
 export(NodeList)
-export(Partition)
 export(Partitions)
 export(TwoByTwoTable)
 export(adjustToViewport)
@@ -45,6 +43,7 @@ export(findViewport)
 export(fishersTest)
 export(getDuplicateLinks)
 export(getIsolatedNodes)
+export(getPartitionIndex)
 export(getQuadrantValues)
 export(heatmap)
 export(heatmap.dt)
@@ -76,8 +75,8 @@ export(sensitivity)
 export(smoothedMean)
 export(specificity)
 export(writeJSON)
+export(writeNetworkJSON)
 exportClasses(ContingencyTable)
-exportClasses(KPartiteNetwork)
 exportClasses(Link)
 exportClasses(LinkList)
 exportClasses(Network)
@@ -87,6 +86,12 @@ exportClasses(NodeIdList)
 exportClasses(NodeList)
 exportClasses(Partitions)
 exportClasses(TwoByTwoTable)
+exportMethods(KPartiteNetwork)
+exportMethods(Link)
+exportMethods(LinkList)
+exportMethods(Network)
+exportMethods(NodeIdList)
+exportMethods(NodeList)
 exportMethods(allStats)
 exportMethods(chiSqResults)
 exportMethods(fishersTest)
@@ -106,6 +111,7 @@ exportMethods(relativeRisk)
 exportMethods(sensitivity)
 exportMethods(specificity)
 exportMethods(toJSON)
+exportMethods(writeNetworkJSON)
 import(data.table)
 import(veupathUtils)
 importFrom(S4Vectors,SimpleList)

R/constructors-Node.R

@@ -100,30 +100,27 @@ setMethod("NodeIdList", "Node", function(object, uniquifyIds = c(TRUE, FALSE)) {
 #' @param y numeric value indicating the y coordinate of the node. Optional.
 #' @param color string or numeric that determines the color of the node. Optional.
 #' @param weight numeric value associated with the node, such as timestamp or other node-associated data. Optional.
-#' @export
+#' @param degree numeric value indicating the degree of the node. This only makes sense in the context of a network,
+#'    and should not be provided in other contexts like when working w an individual node.
 setGeneric("Node", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) standardGeneric("Node"), signature = c("id"))
 
-#' @export
 setMethod("Node", "numeric", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
-  degree <- ifelse(is.null(degree), 0, degree)
+  degree <- ifelse(is.null(degree), NA_real_, degree)
   new("Node", id = NodeId(as.character(id)), x = x, y = y, color = color, weight = weight, degree = degree)
 })
 
-#' @export
 setMethod("Node", "character", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
-  degree <- ifelse(is.null(degree), 0, degree)
+  degree <- ifelse(is.null(degree), NA_real_, degree)
   new("Node", id = NodeId(id), x = x, y = y, color = color, weight = weight, degree = degree)
 })
 
-#' @export
 setMethod("Node", "NodeId", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
-  degree <- ifelse(is.null(degree), 0, degree)
+  degree <- ifelse(is.null(degree), NA_real_, degree)
   new("Node", id = id, x = x, y = y, color = color, weight = weight, degree = degree)
 })
 
-#' @export 
 setMethod("Node", "missing", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
-  degree <- ifelse(is.null(degree), 0, degree)
+  degree <- ifelse(is.null(degree), NA_real_, degree)
   new("Node", id = NodeId(generate_node_id(1)), x = x, y = y, color = color, weight = weight, degree = degree)
 })
 

R/methods-Network.R

@@ -194,17 +194,17 @@ setMethod(toJSONGeneric, "Network", function(object, named = c(TRUE, FALSE)) {
   return(tmp)
 })
 
-#' Write json to tmp file
+#' Write network json to tmp file
 #' 
 #' This function returns the name of a json file which it has
 #' written an object out to.
 #' @param x an object to convert to json and write to a tmp file
 #' @param verbose boolean that declares if logging is desired
 #' @return character name of a tmp file w ext *.json
 #' @export
-setGeneric("writeJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) standardGeneric("writeJSON"))
+setGeneric("writeNetworkJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) standardGeneric("writeNetworkJSON"))
 
-#' Write json to local tmp file
+#' Write network json to local tmp file
 #'
 #' This function returns the name of a json file which it has
 #' written a Network object out to.
@@ -214,7 +214,7 @@ setGeneric("writeJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) st
 #' @return character name of a tmp file w ext *.json
 #' @importFrom jsonlite toJSON
 #' @export
-setMethod("writeJSON", "Network", function(x, pattern=NULL, verbose = c(TRUE, FALSE)) {
+setMethod("writeNetworkJSON", "Network", function(x, pattern=NULL, verbose = c(TRUE, FALSE)) {
   net <- x
   verbose <- veupathUtils::matchArg(verbose)
 

R/methods-Nodes.R

@@ -72,7 +72,7 @@ setMethod(toJSONGeneric, "Node", function(object, named = c(FALSE, TRUE)) {
     if (!!length(y(object)) && !is.na(y(object))) tmp <- paste0(tmp, ',"y":', jsonlite::toJSON(jsonlite::unbox(y(object))))
     if (!!length(color(object))) tmp <- paste0(tmp, ',"color":', jsonlite::toJSON(jsonlite::unbox(color(object))))
     if (!!length(weight(object))) tmp <- paste0(tmp, ',"weight":', jsonlite::toJSON(jsonlite::unbox(weight(object))))
-    if (!!length(degree(object))) tmp <- paste0(tmp, ',"degree":', jsonlite::toJSON(jsonlite::unbox(degree(object))))
+    if (!!length(degree(object)) && !is.na(degree(object))) tmp <- paste0(tmp, ',"degree":', jsonlite::toJSON(jsonlite::unbox(degree(object))))
 
     tmp <- paste0('{', tmp, '}')
     if (named) {