diff --git a/DESCRIPTION b/DESCRIPTION
index 5b5ee0b..dfc8a14 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -34,7 +34,7 @@ Description: plot.data is an R package for creating client-ready data for variou
 License: Apache License (= 2.0)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     covr,
     testthat (>= 2.1.0)
diff --git a/NAMESPACE b/NAMESPACE
index e9bab98..03e79f2 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/class-Link.R b/R/class-Link.R
index 991c0bd..08b0fca 100644
--- a/R/class-Link.R
+++ b/R/class-Link.R
@@ -17,7 +17,6 @@ check_link <- function(object) {
   return(if (length(errors) == 0) TRUE else errors) 
 }
 
-
 #' Link
 #' 
 #' Represent one singular link. A link has a source, and a target. It may be directed or undirected.
@@ -30,16 +29,16 @@ check_link <- function(object) {
 #' @export
 setClass("Link", 
   representation(
-    source = "Node",
-    target = "Node",
+    source = "NodeId",
+    target = "NodeId",
     weight = "numeric",
     color = 'ANY',
     isDirected = "logical"
     # label = "character" # coming soon
   ),
   prototype = prototype(
-    source = Node(),
-    target = Node(),
+    source = NodeId(),
+    target = NodeId(),
     weight = 1,
     color = NULL,
     isDirected = FALSE
@@ -49,8 +48,8 @@ setClass("Link",
 
 #' Link constructor
 #' 
-#' @param source The source node
-#' @param target The target node
+#' @param source The source node identifier
+#' @param target The target node identifier
 #' @param weight The weight of the link
 #' @param color The color of the link
 #' @param isDirected Whether the link is directed
@@ -59,22 +58,22 @@ setGeneric("Link", function(source, target, weight = 1, color = NULL, isDirected
 
 #' @export
 setMethod("Link", c("Node", "Node"), function(source, target, weight = 1, color = NULL, isDirected = FALSE) {
-  new("Link", source = source, target = target, weight = weight, color = color, isDirected = isDirected)
+  new("Link", source = NodeId(id(source)), target = NodeId(id(target)), weight = weight, color = color, isDirected = isDirected)
 })
 
 #' @export
 setMethod("Link", c("character", "character"), function(source, target, weight = 1, color = NULL, isDirected = FALSE) {
-  Link(source = Node(source), target = Node(target), weight = weight, color = color, isDirected = isDirected)
+  Link(source = NodeId(source), target = NodeId(target), weight = weight, color = color, isDirected = isDirected)
 })
 
 #' @export
 setMethod("Link", c("numeric", "numeric"), function(source, target, weight = 1, color = NULL, isDirected = FALSE) {
-  Link(source = Node(source), target = Node(target), weight = weight, color = color, isDirected = isDirected)
+  Link(source = NodeId(source), target = NodeId(target), weight = weight, color = color, isDirected = isDirected)
 })
 
 #' @export
 setMethod("Link", c("NodeId", "NodeId"), function(source, target, weight = 1, color = NULL, isDirected = FALSE) {
-  Link(source = Node(source), target = Node(target), weight = weight, color = color, isDirected = isDirected)
+  new("Link", source = source, target = target, weight = weight, color = color, isDirected = isDirected)
 })
 
 #' @export
diff --git a/R/class-Network.R b/R/class-Network.R
index e994bd3..4d3b6a0 100644
--- a/R/class-Network.R
+++ b/R/class-Network.R
@@ -4,7 +4,7 @@ check_network <- function(object) {
   errors <- character()
 
   # Check that all nodes in links are in nodes
-  nodesInLinks <- NodeList(union(getSourceNodes(object@links), getTargetNodes(object@links))) # may become a method later if i find i use it elsewhere
+  nodesInLinks <- NodeIdList(union(getSourceNodes(object@links), getTargetNodes(object@links))) # may become a method later if i find i use it elsewhere
   if (!all(getNodeIds(nodesInLinks) %in% getNodeIds(object@nodes))) {
     errors <- c(errors, 'Found a node in a link that is not in the node list. All nodes in links must also be in nodes.')
   }
diff --git a/R/class-Node.R b/R/class-Node.R
index e3dabd1..5e1c37b 100644
--- a/R/class-Node.R
+++ b/R/class-Node.R
@@ -103,6 +103,7 @@ generate_node_id <- function(n = 5000) {
 #' @slot y numeric value indicating the y coordinate of the node. Optional.
 #' @slot color string or numeric that determines the color of the node. Optional.
 #' @slot weight numeric value associated with the node, such as timestamp or other node-associated data. Optional.
+#' @slot degree numeric value indicating the degree of the node
 #' 
 #' @name Node-class
 #' @rdname Node-class
@@ -113,7 +114,8 @@ setClass("Node",
     x = "numeric",
     y = "numeric",
     color = "ANY",
-    weight = "ANY"
+    weight = "ANY",
+    degree = "numeric"
   ),
   validity = check_node
 )
diff --git a/R/constructors-Node.R b/R/constructors-Node.R
index 9b7a147..e996914 100644
--- a/R/constructors-Node.R
+++ b/R/constructors-Node.R
@@ -6,8 +6,11 @@
 #' 
 #' @param value string a unique identifier for the node
 #' @export 
-NodeId <- function(value) {
-  new("NodeId", value = value)
+NodeId <- function(value = character()) {
+  if (length(value) == 0) {
+    value <- generate_node_id(1)
+  }
+  new("NodeId", value = as.character(value))
 }
 
 
@@ -97,27 +100,28 @@ 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
-setGeneric("Node", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL) standardGeneric("Node"), signature = c("id"))
+#' @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) {
-  new("Node", id = NodeId(as.character(id)), x = x, y = y, color = color, weight = weight)
+setMethod("Node", "numeric", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
+  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) {
-  new("Node", id = NodeId(id), x = x, y = y, color = color, weight = weight)
+setMethod("Node", "character", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
+  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) {
-  new("Node", id = id, x = x, y = y, color = color, weight = weight)
+setMethod("Node", "NodeId", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
+  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) {
-  new("Node", id = NodeId(generate_node_id(1)), x = x, y = y, color = color, weight = weight)
+setMethod("Node", "missing", function(id, x = numeric(), y = numeric(), color = NULL, weight = NULL, degree = NULL) {
+  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)
 })
 
 
@@ -138,8 +142,13 @@ setMethod("NodeList", "data.frame", function(object = data.frame(source=characte
     stop(paste("Invalid edgeList:", isValidEdgeList(object), collapse = '\n'))
   }
   
-  allNodeIds <- unique(c(object$source, object$target))
-  nodesList <- lapply(allNodeIds, Node)
+  allNodeIds <- c(object$source, object$target)
+
+  makeNodeWithDegree <- function(nodeId, allNodeIds) {
+    new("Node", id = NodeId(nodeId), degree = length(which(allNodeIds == nodeId)))
+  }
+
+  nodesList <- lapply(unique(allNodeIds), makeNodeWithDegree, allNodeIds)
   new("NodeList", nodesList)
 })
 
diff --git a/R/methods-KPartiteNetwork.R b/R/methods-KPartiteNetwork.R
index 504f264..0bc7769 100644
--- a/R/methods-KPartiteNetwork.R
+++ b/R/methods-KPartiteNetwork.R
@@ -41,8 +41,6 @@ setMethod(toJSONGeneric, "KPartiteNetwork", function(object, named = c(TRUE, FAL
     links_json <- veupathUtils::toJSON(object@links, named = FALSE)
     partitions_json <- veupathUtils::toJSON(object@partitions, named = FALSE)
     
-    # TODO this doesnt conform to the api in the data service, bc there we explicitly have a bipartite network and not a kpartite
-    # we have `columns1NodeIds` and `columns2NodeIds` instead of `partitions`. i think this is better though.
     tmp <- paste0('"nodes":', nodes_json, ',"links":', links_json, ',"partitions":', partitions_json)
     tmp <- paste0('"data":{', tmp, '}')
     tmp <- paste0('{', tmp, ',"config":{"variables":{', veupathUtils::toJSON(object@variableMapping, named = FALSE), '}}}')
diff --git a/R/methods-Network.R b/R/methods-Network.R
index ab48bea..ad06098 100644
--- a/R/methods-Network.R
+++ b/R/methods-Network.R
@@ -11,6 +11,7 @@ setGeneric("getLinkColorScheme", function(object) standardGeneric("getLinkColorS
 setMethod("getLinkColorScheme", "Network", function(object) object@linkColorScheme)
 # No setters! Once created, a network should only be updated via network methods
 
+setMethod("getDegrees", "Network", function(object) getDegrees(getNodes(object)))
 
 ## General network methods
 
@@ -26,8 +27,8 @@ setMethod("getIsolatedNodes", "Network", function(net) {
   nodes <- getNodes(net)
   links <- getLinks(net)
 
-  nodesWithLinks <- NodeList(union(getSourceNodes(links), getTargetNodes(links)))
-  isolatedNodeIds <- setdiff(getNodeIds(nodes), getNodeIds(nodesWithLinks))
+  nodeIdsWithLinks <- NodeIdList(union(getSourceNodes(links), getTargetNodes(links)))
+  isolatedNodeIds <- setdiff(getNodeIds(nodes), getNodeIds(nodeIdsWithLinks))
   isolatedNodes <- NodeList(nodes[which(getNodeIds(nodes) %in% isolatedNodeIds)])
 
   return(isolatedNodes)
@@ -192,7 +193,7 @@ 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.
@@ -200,9 +201,9 @@ setMethod(toJSONGeneric, "Network", function(object, named = c(TRUE, FALSE)) {
 #' @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.
@@ -212,7 +213,7 @@ 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)
 
diff --git a/R/methods-Nodes.R b/R/methods-Nodes.R
index 6be5603..7585300 100644
--- a/R/methods-Nodes.R
+++ b/R/methods-Nodes.R
@@ -8,6 +8,8 @@ setGeneric("x", function(object) standardGeneric("x"))
 setGeneric("x<-", function(object, value) standardGeneric("x<-"))
 setGeneric("y", function(object) standardGeneric("y"))
 setGeneric("y<-", function(object, value) standardGeneric("y<-"))
+setGeneric("degree", function(object) standardGeneric("degree"))
+setGeneric("degree<-", function(object, value) standardGeneric("degree<-"))
 
 #' @include methods-Links.R
 ## Methods for Nodes
@@ -21,6 +23,8 @@ setMethod("x<-", "Node", function(object, value) {object@x <- value; validObject
 setMethod("y<-", "Node", function(object, value) {object@y <- value; validObject(object); object})
 setMethod("color<-", "Node", function(object, value) {object@color <- value; validObject(object); object})
 setMethod("weight<-", "Node", function(object, value) {object@weight <- value; validObject(object); object})
+setMethod("degree", "Node", function(object) object@degree)
+setMethod("degree<-", "Node", function(object, value) {object@degree <- value; validObject(object); object})
 
 ## Methods for NodeId
 setMethod("id", "NodeId", function(object) object@value)
@@ -36,6 +40,8 @@ setGeneric("getNodeIds", function(object) standardGeneric("getNodeIds"))
 setMethod("getNodeIds", "NodeList", function(object) unlist(lapply(as.list(object), id)))
 setMethod("getWeights", "NodeList", function(object) unlist(lapply(as.list(object), weight)))
 setMethod("getColors", "NodeList", function(object) unlist(lapply(as.list(object), color)))
+setGeneric("getDegrees", function(object) standardGeneric("getDegrees"))
+setMethod("getDegrees", "NodeList", function(object) unlist(lapply(as.list(object), degree)))
 
 ## Methods for NodeIdList
 setMethod("getNodeIds", "NodeIdList", function(object) unlist(lapply(as.list(object), id)))
@@ -58,6 +64,7 @@ setMethod(toJSONGeneric, "Node", function(object, named = c(FALSE, TRUE)) {
     if (!!length(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)) && !is.na(degree(object))) tmp <- paste0(tmp, ',"degree":', jsonlite::toJSON(jsonlite::unbox(degree(object))))
 
     tmp <- paste0('{', tmp, '}')
     if (named) {
diff --git a/man/KPartiteNetwork-class.Rd b/man/KPartiteNetwork-class.Rd
index c998bdd..021a005 100644
--- a/man/KPartiteNetwork-class.Rd
+++ b/man/KPartiteNetwork-class.Rd
@@ -1,10 +1,20 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/class-KPartiteNetwork.R
-\docType{class}
 \name{KPartiteNetwork-class}
 \alias{KPartiteNetwork-class}
 \alias{KPartiteNetwork}
 \title{k-Partite Network}
+\usage{
+KPartiteNetwork(
+  object,
+  links,
+  nodes,
+  partitions = Partitions(),
+  linkColorScheme = "none",
+  variables = VariableMetadataList(),
+  ...
+)
+}
 \description{
 The k-partite network class represents data in the form of a network with k distinct groups of nodes
 in which nodes connect only with nodes from the other groups. In other words, there are only inter-group
diff --git a/man/Link-class.Rd b/man/Link-class.Rd
index 78c8efa..d1b742e 100644
--- a/man/Link-class.Rd
+++ b/man/Link-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Link-class}
 \alias{Link-class}
-\alias{Link}
 \title{Link}
 \description{
 Represent one singular link. A link has a source, and a target. It may be directed or undirected.
diff --git a/man/Link.Rd b/man/Link.Rd
new file mode 100644
index 0000000..9342f27
--- /dev/null
+++ b/man/Link.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Link.R
+\name{Link}
+\alias{Link}
+\title{Link constructor}
+\usage{
+Link(source, target, weight = 1, color = NULL, isDirected = FALSE)
+}
+\arguments{
+\item{source}{The source node identifier}
+
+\item{target}{The target node identifier}
+
+\item{weight}{The weight of the link}
+
+\item{color}{The color of the link}
+
+\item{isDirected}{Whether the link is directed}
+}
+\description{
+Link constructor
+}
diff --git a/man/LinkList-class.Rd b/man/LinkList-class.Rd
index e5b8502..efca045 100644
--- a/man/LinkList-class.Rd
+++ b/man/LinkList-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{LinkList-class}
 \alias{LinkList-class}
-\alias{LinkList}
 \title{Link List}
 \description{
 A class for representing links in a network
diff --git a/man/LinkList.Rd b/man/LinkList.Rd
new file mode 100644
index 0000000..ca7762e
--- /dev/null
+++ b/man/LinkList.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Link.R
+\name{LinkList}
+\alias{LinkList}
+\title{Generate a LinkList}
+\usage{
+LinkList(object, linkColorScheme = c("none", "posneg"))
+}
+\arguments{
+\item{object}{Object containing data to be converted to a LinkList. Could be a SimpleList of Links or a data.frame
+with columns source, target, and optionally weight and color.}
+
+\item{linkColorScheme}{Either 'none' or 'posneg'. If 'posneg', the link color will be based on the sign of the weight.}
+}
+\value{
+LinkList
+}
+\description{
+Generate a LinkList from an edgeList
+}
+\examples{
+LinkList(data.frame(source='a',target='b'))
+}
diff --git a/man/Network-class.Rd b/man/Network-class.Rd
index ab77309..da6de68 100644
--- a/man/Network-class.Rd
+++ b/man/Network-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Network-class}
 \alias{Network-class}
-\alias{Network}
 \title{Network}
 \description{
 A class for representing networks. A network is composed of nodes and links (edges, connections, etc.). A link is represented
@@ -17,9 +16,10 @@ in case some nodes have no links. A network can also have properties such as dir
 
 \item{\code{nodes}}{NodeList object defining the nodes in the network. Some nodes may not have any links.}
 
-\item{\code{linkColorScheme}}{string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'.}
-
-\item{\code{variableMapping}}{veupathUtils::VariableMetadataList object defining the variable mappings in the network.
+\item{\code{linkColorScheme}}{string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'.
+In the case of 'posneg', the links color slot will be set to 1 if the link is positive, and -1 if the link is negative.
 Use a method assignLinkColors() to assign colors to links and set this slot's value.}
+
+\item{\code{variableMapping}}{veupathUtils::VariableMetadataList object defining the variable mappings in the network.}
 }}
 
diff --git a/man/Node-class.Rd b/man/Node-class.Rd
index f62ec59..6a7727f 100644
--- a/man/Node-class.Rd
+++ b/man/Node-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Node-class}
 \alias{Node-class}
-\alias{Node}
 \title{Node}
 \description{
 A class for representing nodes in a network
@@ -20,5 +19,7 @@ A class for representing nodes in a network
 \item{\code{color}}{string or numeric that determines the color of the node. Optional.}
 
 \item{\code{weight}}{numeric value associated with the node, such as timestamp or other node-associated data. Optional.}
+
+\item{\code{degree}}{numeric value indicating the degree of the node}
 }}
 
diff --git a/man/Node.Rd b/man/Node.Rd
new file mode 100644
index 0000000..6a7fbc0
--- /dev/null
+++ b/man/Node.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/constructors-Node.R
+\name{Node}
+\alias{Node}
+\title{Create a Node}
+\usage{
+Node(
+  id,
+  x = numeric(),
+  y = numeric(),
+  color = NULL,
+  weight = NULL,
+  degree = NULL
+)
+}
+\arguments{
+\item{id}{string, NodeId or numeric: a unique identifier for the node}
+
+\item{x}{numeric value indicating the x coordinate of the node. Optional.}
+
+\item{y}{numeric value indicating the y coordinate of the node. Optional.}
+
+\item{color}{string or numeric that determines the color of the node. Optional.}
+
+\item{weight}{numeric value associated with the node, such as timestamp or other node-associated data. Optional.}
+
+\item{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.}
+}
+\description{
+Create a Node given a unique identifier as either string, NodeId or numeric.
+}
diff --git a/man/NodeId.Rd b/man/NodeId.Rd
deleted file mode 100644
index f8d1b16..0000000
--- a/man/NodeId.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-Node.R
-\name{NodeId}
-\alias{NodeId}
-\title{Create a Node Id}
-\usage{
-NodeId(value)
-}
-\arguments{
-\item{value}{string a unique identifier for the node}
-}
-\description{
-Because typing `NodeId(id = 'foo')` is annoying, this function is provided
-to make things easier. Now you can do `NodeId('foo')`
-}
diff --git a/man/NodeIdList.Rd b/man/NodeIdList.Rd
index 6ddb4a3..aa51c89 100644
--- a/man/NodeIdList.Rd
+++ b/man/NodeIdList.Rd
@@ -1,13 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-Node.R
+% Please edit documentation in R/constructors-Node.R
 \name{NodeIdList}
 \alias{NodeIdList}
 \title{Create a NodeIdList}
 \usage{
-NodeIdList(nodeIds)
+NodeIdList(object, uniquifyIds = c(TRUE, FALSE))
 }
 \arguments{
-\item{nodeIds}{list of node ids}
+\item{object}{Object containing list of node ids}
+
+\item{uniquifyIds}{Logical indicating whether to uniquify the node ids}
 }
 \description{
 Create a NodeIdList
diff --git a/man/NodeList-class.Rd b/man/NodeList-class.Rd
index e02ead8..76f945c 100644
--- a/man/NodeList-class.Rd
+++ b/man/NodeList-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{NodeList-class}
 \alias{NodeList-class}
-\alias{NodeList}
 \title{NodeList}
 \description{
 A class for representing a list of nodes.
diff --git a/man/Partition-class.Rd b/man/Partition-class.Rd
index 9ad0e46..22fc7ad 100644
--- a/man/Partition-class.Rd
+++ b/man/Partition-class.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \name{Partition-class}
 \alias{Partition-class}
 \alias{Partition}
 \title{Create a Partition}
 \usage{
-Partition(nodeIds)
+NodeIdList(object, uniquifyIds = c(TRUE, FALSE))
 }
 \description{
 An alias to NodeIdList
diff --git a/man/Partitions-class.Rd b/man/Partitions-class.Rd
index 3745ab7..253448c 100644
--- a/man/Partitions-class.Rd
+++ b/man/Partitions-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \docType{class}
 \name{Partitions-class}
 \alias{Partitions-class}
diff --git a/man/Partitions.Rd b/man/Partitions.Rd
index 1d49f22..542eb3e 100644
--- a/man/Partitions.Rd
+++ b/man/Partitions.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \name{Partitions}
 \alias{Partitions}
 \title{Create Partitions}
diff --git a/man/getPartitionIndex.Rd b/man/getPartitionIndex.Rd
new file mode 100644
index 0000000..d4c2200
--- /dev/null
+++ b/man/getPartitionIndex.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Partitions.R
+\name{getPartitionIndex}
+\alias{getPartitionIndex}
+\title{Get Partition index of a Node}
+\usage{
+getPartitionIndex(partitions, node)
+}
+\arguments{
+\item{partitions}{Partitions}
+
+\item{node}{character, NodeId or Node object}
+}
+\description{
+Given a list of partitions and a node id, return the index
+of the partition that the node belongs to.
+}
diff --git a/man/toJSON-KPartiteNetwork-method.Rd b/man/toJSON-KPartiteNetwork-method.Rd
new file mode 100644
index 0000000..8eebafc
--- /dev/null
+++ b/man/toJSON-KPartiteNetwork-method.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-KPartiteNetwork.R
+\name{toJSON,KPartiteNetwork-method}
+\alias{toJSON,KPartiteNetwork-method}
+\title{Convert KPartiteNetwork object to JSON}
+\usage{
+\S4method{toJSON}{KPartiteNetwork}(object, named = c(TRUE, FALSE))
+}
+\arguments{
+\item{object}{A KPartiteNetwork object}
+
+\item{named}{boolean that declares if names should be included}
+}
+\description{
+Converts a KPartiteNetwork object to JSON
+}
diff --git a/man/toJSON-Partitions-method.Rd b/man/toJSON-Partitions-method.Rd
new file mode 100644
index 0000000..693c5e0
--- /dev/null
+++ b/man/toJSON-Partitions-method.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-KPartiteNetwork.R
+\name{toJSON,Partitions-method}
+\alias{toJSON,Partitions-method}
+\title{Convert Partitions object to JSON}
+\usage{
+\S4method{toJSON}{Partitions}(object, named = c(TRUE, FALSE))
+}
+\arguments{
+\item{object}{A Partitions object}
+
+\item{named}{boolean that declares if names should be included}
+}
+\description{
+Converts a Partitions object to JSON
+}
diff --git a/man/writeJSON.Rd b/man/writeJSON.Rd
index 539bffa..87b63f8 100644
--- a/man/writeJSON.Rd
+++ b/man/writeJSON.Rd
@@ -1,38 +1,20 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/methods-Network.R, R/utils-json.R
+% Please edit documentation in R/utils-json.R
 \name{writeJSON}
 \alias{writeJSON}
-\title{Write json to tmp file}
+\title{Write json to local tmp file}
 \usage{
-writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
-
-writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
-
 writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
 }
 \arguments{
 \item{.pd}{a data.table to convert to json and write to a tmp file}
 
 \item{pattern}{optional tmp file prefix}
-
-\item{verbose}{boolean that declares if logging is desired}
-
-\item{x}{a data.table to convert to json and write to a tmp file}
 }
 \value{
-character name of a tmp file w ext *.json
-
-character name of a tmp file w ext *.json
-
 character name of a tmp file w ext *.json
 }
 \description{
-This function returns the name of a json file which it has
-written an object out to.
-
-This function returns the name of a json file which it has
-written a Network object out to.
-
 This function returns the name of a json file which it has
 written a data.table object out to.
 }
diff --git a/man/writeNetworkJSON-Network-method.Rd b/man/writeNetworkJSON-Network-method.Rd
new file mode 100644
index 0000000..1872437
--- /dev/null
+++ b/man/writeNetworkJSON-Network-method.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-Network.R
+\name{writeNetworkJSON,Network-method}
+\alias{writeNetworkJSON,Network-method}
+\title{Write network json to local tmp file}
+\usage{
+\S4method{writeNetworkJSON}{Network}(x, pattern = NULL, verbose = c(TRUE, FALSE))
+}
+\arguments{
+\item{x}{a data.table to convert to json and write to a tmp file}
+
+\item{pattern}{optional tmp file prefix}
+
+\item{verbose}{boolean that declares if logging is desired}
+}
+\value{
+character name of a tmp file w ext *.json
+}
+\description{
+This function returns the name of a json file which it has
+written a Network object out to.
+}
diff --git a/man/writeNetworkJSON.Rd b/man/writeNetworkJSON.Rd
new file mode 100644
index 0000000..1f32127
--- /dev/null
+++ b/man/writeNetworkJSON.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-Network.R
+\name{writeNetworkJSON}
+\alias{writeNetworkJSON}
+\title{Write network json to tmp file}
+\usage{
+writeNetworkJSON(x, pattern = NULL, verbose = c(TRUE, FALSE))
+}
+\arguments{
+\item{x}{an object to convert to json and write to a tmp file}
+
+\item{verbose}{boolean that declares if logging is desired}
+}
+\value{
+character name of a tmp file w ext *.json
+}
+\description{
+This function returns the name of a json file which it has
+written an object out to.
+}
diff --git a/tests/testthat/test-kpartite-network.R b/tests/testthat/test-kpartite-network.R
index fd8ec94..84845da 100644
--- a/tests/testthat/test-kpartite-network.R
+++ b/tests/testthat/test-kpartite-network.R
@@ -166,7 +166,7 @@ test_that("we can build a KPartiteNetwork from an edgeList data.frame", {
     ))
   )
 
-  expect_equal(getNodes(net), NodeList(c(Node('a'), Node('b'), Node('c'), Node('d'))))
+  expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=1), Node('d', degree=1))))
   expect_equal(getLinks(net), LinkList(c(Link(source = Node('a'), target = Node('b')), Link(source = Node('b'), target = Node('a')), Link(source = Node('c'), target = Node('d')))))
   expect_equal(partitions(net), Partitions(list(Partition(list(Node('a'), Node('c'))), Partition(list(Node('b'), Node('d'))))))
   expect_equal(getLinkColorScheme(net), 'none')
diff --git a/tests/testthat/test-links.R b/tests/testthat/test-links.R
index 8db2bb0..f89972a 100644
--- a/tests/testthat/test-links.R
+++ b/tests/testthat/test-links.R
@@ -1,56 +1,49 @@
 test_that("Links work", {
   # Make a link
-  nodeA <- Node(
-    id = NodeId('A')
-  )
-  nodeB <- Node(
-    id = NodeId('B')
-  )
-
-  link <- Link(source = nodeA, target = nodeB)
+  link <- Link(source = NodeId('A'), target = NodeId('B'))
   expect_equal(class(link)[1], 'Link')
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
 
   # Make another link w colors and weights
-  link <- Link(source = nodeA, target = nodeB, color = 'red', weight = 10)
+  link <- Link(source = NodeId('A'), target = NodeId('B'), color = 'red', weight = 10)
   expect_equal(class(link)[1], 'Link')
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(color(link), 'red')
   expect_equal(weight(link), 10)
 
   # pass characters for node ids
   link <- Link(source = 'A', target = 'B')
   expect_equal(class(link)[1], 'Link')
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
 
   # pass numbers for node ids
   link <- Link(source = 1, target = 2)
   expect_equal(class(link)[1], 'Link')
-  expect_equal(source(link), Node(1))
-  expect_equal(target(link), Node(2))
+  expect_equal(source(link), NodeId(1))
+  expect_equal(target(link), NodeId(2))
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
 
   # pass NodeId objects for node ids
   link <- Link(source = NodeId('A'), target = NodeId('B'))
   expect_equal(class(link)[1], 'Link')
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
 
   # an empty one
   link <- Link()
   expect_equal(class(link)[1], 'Link')
-  expect_equal(class(source(link))[1], 'Node')
-  expect_equal(class(target(link))[1], 'Node')
+  expect_equal(class(source(link))[1], 'NodeId')
+  expect_equal(class(target(link))[1], 'NodeId')
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
 })
@@ -65,15 +58,15 @@ test_that("Link methods work", {
   )
 
   link <- Link(source = nodeA, target = nodeB)
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(weight(link), 1)
   expect_true(is.null(color(link)))
   expect_equal(isDirected(link), FALSE)
 
   link <- Link(source = nodeA, target = nodeB, color = 'red', weight = 10)
-  expect_equal(source(link), nodeA)
-  expect_equal(target(link), nodeB)
+  expect_equal(source(link), NodeId('A'))
+  expect_equal(target(link), NodeId('B'))
   expect_equal(color(link), 'red')
   expect_equal(weight(link), 10)
   expect_equal(isDirected(link), FALSE)
@@ -100,8 +93,8 @@ test_that("LinkList methods work", {
 
   linkList <- LinkList(S4Vectors::SimpleList(c(link1, link2, link3)))
   expect_equal(length(linkList), 3)
-  expect_equal(getSourceNodes(linkList), list(nodeA, nodeB, nodeC))
-  expect_equal(getTargetNodes(linkList), list(nodeB, nodeC, nodeA))
+  expect_equal(getSourceNodes(linkList), list(NodeId('A'), NodeId('B'), NodeId('C')))
+  expect_equal(getTargetNodes(linkList), list(NodeId('B'), NodeId('C'), NodeId('A')))
   expect_equal(getWeights(linkList), c(1, 1, 1))
   expect_equal(getColors(linkList), c(NULL, NULL, NULL))
 
@@ -113,16 +106,16 @@ test_that("LinkList methods work", {
 
   linkList <- LinkList(S4Vectors::SimpleList(c(link1, link2, link3)))
   expect_equal(length(linkList), 3)
-  expect_equal(getSourceNodes(linkList), list(nodeA, nodeB, nodeC))
-  expect_equal(getTargetNodes(linkList), list(nodeB, nodeC, nodeA))
+  expect_equal(getSourceNodes(linkList), list(NodeId('A'), NodeId('B'), NodeId('C')))
+  expect_equal(getTargetNodes(linkList), list(NodeId('B'), NodeId('C'), NodeId('A')))
   expect_equal(getWeights(linkList), c(2, 0.1, 3))
   expect_equal(getColors(linkList), c('red', 'blue', 'green'))
 
   # use a list to make LinkList
   linkList <- LinkList(list(link1, link2, link3))
   expect_equal(length(linkList), 3)
-  expect_equal(getSourceNodes(linkList), list(nodeA, nodeB, nodeC))
-  expect_equal(getTargetNodes(linkList), list(nodeB, nodeC, nodeA))
+  expect_equal(getSourceNodes(linkList), list(NodeId('A'), NodeId('B'), NodeId('C')))
+  expect_equal(getTargetNodes(linkList), list(NodeId('B'), NodeId('C'), NodeId('A')))
   expect_equal(getWeights(linkList), c(2, 0.1, 3))
   expect_equal(getColors(linkList), c('red', 'blue', 'green'))
 
diff --git a/tests/testthat/test-network.R b/tests/testthat/test-network.R
index 63a359c..78937f6 100644
--- a/tests/testthat/test-network.R
+++ b/tests/testthat/test-network.R
@@ -147,13 +147,16 @@ test_that("We can remove links by weight", {
 test_that("toJSON works for networks", {
   # Create some nodes
   nodeA <- Node(
-    id = NodeId('A')
+    id = NodeId('A'),
+    degree = 2
   )
   nodeB <- Node(
-    id = NodeId('B')
+    id = NodeId('B'),
+    degree = 2
   )
   nodeC <- Node(
-    id = NodeId('C')
+    id = NodeId('C'),
+    degree = 2
   )
   
   # Create some links
@@ -169,6 +172,7 @@ test_that("toJSON works for networks", {
   expect_equal(jsonList$network$data$links$target, c('B','C','A'))
   expect_equal(jsonList$network$data$links$weight, c(10,20,30))
   expect_equal(jsonList$network$data$nodes$id, c('A','B','C'))
+  expect_equal(jsonList$network$data$nodes$degree, c(2,2,2))
   expect_equal(length(jsonList$network$config$variables), 0)
 
 })
@@ -179,14 +183,15 @@ test_that("we can build a Network from an edgeList data.frame", {
     target = c('b', 'c', 'a')
   )
   net <- Network(object = edgeList)
-  expect_equal(getNodes(net), NodeList(c(Node('a'), Node('b'), Node('c'))))
-  expect_equal(getLinks(net)[[1]]@source, Node('a'))
-  expect_equal(getLinks(net)[[1]]@target, Node('b'))
-  expect_equal(getLinks(net)[[2]]@source, Node('b'))
-  expect_equal(getLinks(net)[[2]]@target, Node('c'))
-  expect_equal(getLinks(net)[[3]]@source, Node('c'))
-  expect_equal(getLinks(net)[[3]]@target, Node('a'))
+  expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
+  expect_equal(getLinks(net)[[1]]@source, NodeId('a'))
+  expect_equal(getLinks(net)[[1]]@target, NodeId('b'))
+  expect_equal(getLinks(net)[[2]]@source, NodeId('b'))
+  expect_equal(getLinks(net)[[2]]@target, NodeId('c'))
+  expect_equal(getLinks(net)[[3]]@source, NodeId('c'))
+  expect_equal(getLinks(net)[[3]]@target, NodeId('a'))
   expect_equal(getLinkColorScheme(net), 'none')
+  expect_equal(getDegrees(net), c(2, 2, 2))
 
   #w a weight column
   edgeList <- data.frame(
@@ -195,10 +200,11 @@ test_that("we can build a Network from an edgeList data.frame", {
     weight = c(1,2,3)
   )
   net <- Network(object = edgeList)
-  expect_equal(getNodes(net), NodeList(c(Node('a'), Node('b'), Node('c'))))
+  expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
   expect_equal(getLinks(net)[[2]]@weight, 2)
   expect_equal(getLinks(net)[[3]]@weight, 3)
   expect_equal(getLinkColorScheme(net), 'none')
+  expect_equal(getDegrees(net), c(2, 2, 2))
 
   #w a color scheme
   edgeList <- data.frame(
@@ -207,7 +213,7 @@ test_that("we can build a Network from an edgeList data.frame", {
     weight = c(-10,0,10)
   )
   net <- Network(object = edgeList, linkColorScheme = 'posneg')
-  expect_equal(getNodes(net), NodeList(c(Node('a'), Node('b'), Node('c'))))
+  expect_equal(getNodes(net), NodeList(c(Node('a', degree=2), Node('b', degree=2), Node('c', degree=2))))
   expect_equal(getLinks(net)[[1]]@weight, -10)
   expect_equal(getLinks(net)[[2]]@weight, 0)
   expect_equal(getLinks(net)[[3]]@weight, 10)
@@ -215,4 +221,5 @@ test_that("we can build a Network from an edgeList data.frame", {
   expect_equal(getLinks(net)[[2]]@color, 0)
   expect_equal(getLinks(net)[[3]]@color, 1)
   expect_equal(getLinkColorScheme(net), 'posneg')
+  expect_equal(getDegrees(net), c(2, 2, 2))
 })
\ No newline at end of file
diff --git a/tests/testthat/test-nodes.R b/tests/testthat/test-nodes.R
index a7adf22..3527eed 100644
--- a/tests/testthat/test-nodes.R
+++ b/tests/testthat/test-nodes.R
@@ -107,6 +107,15 @@ test_that("NodeList methods work", {
   edgeList <- data.frame(source = 'A', target = 'B')
   expect_equal(class(NodeList(edgeList))[1], 'NodeList')
 
+  # multiple edges in edgeList, test degrees
+  edgeList <- data.frame(source = c('A', 'B'), target = c('B', 'C'))
+  expect_equal(class(NodeList(edgeList))[1], 'NodeList')
+  expect_equal(length(NodeList(edgeList)), 3)
+  expect_equal(getNodeIds(NodeList(edgeList)), c('A', 'B', 'C'))
+  expect_equal(getWeights(NodeList(edgeList)), c(NULL, NULL, NULL))
+  expect_equal(getColors(NodeList(edgeList)), c(NULL, NULL, NULL))
+  expect_equal(getDegrees(NodeList(edgeList)), c(1, 2, 1))
+
 })
 
 test_that("We cannot make nonsensical nodes", {
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 724f755..10ddc03 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -4,7 +4,7 @@ test_that("numBinsToBinWidth() returns a binWidth that will actually provide the
   binWidth <- numBinsToBinWidth(testDF$entity.int6, 8)
   viewport <- findViewport(testDF$entity.int6, 'NUMBER')
   x <- bin(testDF$entity.int6, binWidth, viewport)
-  expect_equal(data.table::uniqueN(x),5)
+  expect_equal(data.table::uniqueN(x),6)
 
   binWidth <- numBinsToBinWidth(testDF$entity.int6, 1)
   viewport <- findViewport(testDF$entity.int6, 'NUMBER')