inst/unitTests/test_graphToJSON.R

In RCyjs: Display and manipulate graphs in cytoscape.js

library(RUnit)
library(RCyjs)
#------------------------------------------------------------------------------------------------------------------------
printf <- function(...) print(noquote(sprintf(...)))
#------------------------------------------------------------------------------------------------------------------------
# use ~/github/projects/examples/cyjsMinimal/cyjs.html to test out json strings produced here
#------------------------------------------------------------------------------------------------------------------------
if(!exists("g.big")){
   load(system.file(package="RCyjs", "extdata",  "graph.1669nodes_3260edges_challenge_for_converting_to_json.RData"))
   g.big <- g.lo
   }

if(!exists("g.small")){
   print(load(system.file(package="RCyjs", "extdata",  "graph.11nodes.14edges.RData")))
   g.small <- g
   }


#------------------------------------------------------------------------------------------------------------------------
runTests <- function()
{
   test_1_node()
   test_1_node_with_position()
   test_2_nodes()
   test_2_nodes_1_edge()
   test_1_node_2_attributes()
   test_2_nodes_1_edge_2_edgeAttribute()
   test_smallGraphWithAttributes()
   test_2_nodes_2_edges_no_attributes()
   test_20_nodes_20_edges_no_attributes()
   test_200_nodes_200_edges_no_attributes()
   test_2000_nodes_2000_edges_no_attributes()
   test_1669_3260()

   test_dataFramesToJSON_edgeTableOnly_noExtraAttributes(display=FALSE)
   test_dataFramesToJSON_edgeTableOnly_orhpanNodeInNodeTable(display=FALSE)
   test_dataFramesToJSON_edgeTableOnly_addEdgeAttributes(display=FALSE)
   test_dataFramesToJSON_explicitNodePositions(display=FALSE)

   test_unorderedNodeIDs()

} # runTests
#------------------------------------------------------------------------------------------------------------------------
createTestGraph <- function(nodeCount, edgeCount)
{
   elementCount <- nodeCount^2;
   vec <- rep(0, elementCount)

   set.seed(13);
   vec[sample(1:elementCount, edgeCount)] <- 1
   mtx <- matrix(vec, nrow=nodeCount)

   gam <- graphAM(adjMat=mtx, edgemode="directed")

   as(gam, "graphNEL")

} # createTestGraph
#----------------------------------------------------------------------------------------------------
test_1669_3260 <- function(display=FALSE)
{
   printf("--- test_1669_3260")
   g.json <- RCyjs:::.graphToJSON(g.small)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display


   g2 <- fromJSON(g.json, flatten=TRUE)
   checkEquals(lapply(g2$elements, dim), list(nodes=c(11, 27), edges=c(14,4)))

   system.time(  # < 14 seconds elapsed: 1669 nodes, 3260 edges
      g.json <- RCyjs:::.graphToJSON(g.big)
      )

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   checkEquals(lapply(g2$elements, dim), list(nodes=c(1669, 83), edges=c(3260, 4)))

 } # test_1669_3260
#------------------------------------------------------------------------------------------------------------------------
test_2_nodes_2_edges_no_attributes <- function(display=FALSE)
{
   printf("--- test_2_nodes_2_edges_no_attributes")

   g <- createTestGraph(2, 2)
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(2, 3))

 } # test_2_nodes_2_edges_no_attributes
#------------------------------------------------------------------------------------------------------------------------
test_20_nodes_20_edges_no_attributes <- function(display=FALSE)
{
   printf("--- test_20_nodes_20_edges_no_attributes")

   g <- createTestGraph(20, 20)
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(20, 3))

 } # test_2_nodes_2_edges_no_attributes
#------------------------------------------------------------------------------------------------------------------------
test_200_nodes_200_edges_no_attributes <- function(display=FALSE)
{
   printf("--- test_200_nodes_200_edges_no_attributes")

   g <- createTestGraph(200, 200)
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(199, 3))

 } # test_200_nodes_200_edges_no_attributes
#------------------------------------------------------------------------------------------------------------------------
test_2000_nodes_2000_edges_no_attributes <- function(display=FALSE)
{
   printf("--- test_2000_nodes_2000_edges_no_attributes")

   print(system.time({   # 4 seconds
      g <- createTestGraph(2000, 2000)
      g.json <- RCyjs:::.graphToJSON(g)
      }))

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(2000, 3))

 } # test_2000_nodes_2000_edges_no_attributes
#------------------------------------------------------------------------------------------------------------------------
test_1_node <- function(display=FALSE)
{
   printf("--- test_1_node")
   g <- graphNEL(nodes="A", edgemode="directed")
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))

} # test_1_node
#------------------------------------------------------------------------------------------------------------------------
test_1_node_with_position <- function(display=FALSE)
{
   printf("--- test_1_node_with_position")

   g <- graphNEL(nodes="A", edgemode="directed")
   nodeDataDefaults(g, "xPos") <- 0
   nodeDataDefaults(g, "yPos") <- 0
   nodeData(g, n="A", "xPos") <- pi
   nodeData(g, n="A", "yPos") <- cos(pi)

   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   checkEqualsNumeric(tbl.nodes$data.xPos,  3.1416, tol=1e-4)
   checkEquals(tbl.nodes$position.x,        3.1416, tol=1e-4)
   checkEqualsNumeric(tbl.nodes$data.yPos, -1,      tol=1e-4)
   checkEquals(tbl.nodes$position.y,       -1,      tol=1e-4)

} # test_1_node_with_position
#------------------------------------------------------------------------------------------------------------------------
test_2_nodes <- function(display=FALSE)
{
   printf("--- test_2_nodes")

   g <- graphNEL(nodes=c("A", "B"), edgemode="directed")
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))

} # test_2_nodes
#------------------------------------------------------------------------------------------------------------------------
test_2_nodes_1_edge <- function(display=FALSE)
{
   printf("--- test_2_nodes_1_edge")

   g <- graphNEL(nodes=c("X", "Y"), edgemode="directed")
   g <- addEdge("X", "Y", g);
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

      #  flatten: automatically ‘flatten’ nested data frames into a single non-nested data frame
   g2 <- fromJSON(g.json, flatten=TRUE)
   checkEquals(names(g2$elements), c("nodes", "edges"))
   tbl.nodes <- g2$elements$nodes
   checkEquals(dim(tbl.nodes), c(2,1))
   checkEquals(tbl.nodes$data.id, c("X", "Y"))

   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(1,3))
   checkEquals(tbl.edges$data.id, "X->Y")

} # test_2_nodes_1_edge
#------------------------------------------------------------------------------------------------------------------------
test_1_node_2_attributes <- function(display=FALSE)
{
   printf("--- test_1_node_2_attributse")

   g <- graphNEL(nodes="A", edgemode="directed")
   nodeDataDefaults(g, "size") <- 0
   nodeData(g, "A", "size") <- 99

   nodeDataDefaults(g, "label") <- ""
   nodeData(g, "A", "label") <- "bigA"

   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   tbl.nodes <- g2$elements$nodes
   checkEquals(tbl.nodes$data.id, nodes(g))
   checkEquals(tbl.nodes$data.size, 99)
   checkEquals(tbl.nodes$data.label, "bigA")

} # test_1_node_2_attributes
#------------------------------------------------------------------------------------------------------------------------
test_2_nodes_1_edge_2_edgeAttribute <- function(display=FALSE)
{
   printf("--- test_2_nodes_2_edgeAttributes")

   g <- graphNEL(nodes=c("X", "Y"), edgemode="directed")
   g <- addEdge("X", "Y", g);
   edgeDataDefaults(g, "weight") <- 0
   edgeDataDefaults(g, "edgeType") <- "generic"
   edgeData(g, "X", "Y", "weight") <- 1.234
   edgeData(g, "X", "Y", "edgeType") <- "regulates"

   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

      #  flatten: automatically ‘flatten’ nested data frames into a single non-nested data frame
   g2 <- fromJSON(g.json, flatten=TRUE)
   checkEquals(names(g2$elements), c("nodes", "edges"))
   tbl.nodes <- g2$elements$nodes
   checkEquals(dim(tbl.nodes), c(2,1))
   checkEquals(tbl.nodes$data.id, c("X", "Y"))

   tbl.edges <- g2$elements$edges
   checkEquals(dim(tbl.edges), c(1,5))
   checkEquals(tbl.edges$data.id, "X->Y")
   checkEquals(tbl.edges$data.source, "X")
   checkEquals(tbl.edges$data.target, "Y")
   checkEquals(tbl.edges$data.weight, 1.234)
   checkEquals(tbl.edges$data.edgeType, "regulates")

} # test_2_nodes_1_edge
#------------------------------------------------------------------------------------------------------------------------
test_smallGraphWithAttributes <- function(display=FALSE)
{
   printf("--- test_smallGraphWithAttributes")
   g <- simpleDemoGraph()
   g.json <- RCyjs:::.graphToJSON(g)

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

   g2 <- fromJSON(g.json, flatten=TRUE)
   checkEquals(names(g2$elements), c("nodes", "edges"))
   tbl.nodes <- g2$elements$nodes
   tbl.edges <- g2$elements$edges

   checkEquals(dim(tbl.nodes), c(3, 5))
   checkEquals(colnames(tbl.nodes),
               c("data.id", "data.type", "data.lfc", "data.label", "data.count"))
   checkEquals(dim(tbl.edges), c(3, 6))
   checkEquals(colnames(tbl.edges), c("data.id", "data.source", "data.target", "data.edgeType", "data.score", "data.misc"))

} # test_smallGraphWithAttributes
#------------------------------------------------------------------------------------------------------------------------
simpleDemoGraph = function ()
{
  g = new ('graphNEL', edgemode='directed')

  nodeDataDefaults(g, attr='type') <- 'undefined'
  nodeDataDefaults(g, attr='lfc') <-  1.0
  nodeDataDefaults(g, attr='label') <- 'default node label'
  nodeDataDefaults(g, attr='count') <-  0

  edgeDataDefaults(g, attr='edgeType') <- 'undefined'
  edgeDataDefaults(g, attr='score') <-  0.0
  edgeDataDefaults(g, attr= 'misc') <- "default misc"

  g = graph::addNode ('A', g)
  g = graph::addNode ('B', g)
  g = graph::addNode ('C', g)
  nodeData (g, 'A', 'type') = 'kinase'
  nodeData (g, 'B', 'type') = 'transcription factor'
  nodeData (g, 'C', 'type') = 'glycoprotein'

  nodeData (g, 'A', 'lfc') = -3.0
  nodeData (g, 'B', 'lfc') = 0.0
  nodeData (g, 'C', 'lfc') = 3.0

  nodeData (g, 'A', 'count') = 2
  nodeData (g, 'B', 'count') = 30
  nodeData (g, 'C', 'count') = 100

  nodeData (g, 'A', 'label') = 'Gene A'
  nodeData (g, 'B', 'label') = 'Gene B'
  nodeData (g, 'C', 'label') = 'Gene C'

  g = graph::addEdge ('A', 'B', g)
  g = graph::addEdge ('B', 'C', g)
  g = graph::addEdge ('C', 'A', g)

  edgeData (g, 'A', 'B', 'edgeType') = 'phosphorylates'
  edgeData (g, 'B', 'C', 'edgeType') = 'synthetic lethal'

  edgeData (g, 'A', 'B', 'score') =  35.0
  edgeData (g, 'B', 'C', 'score') =  -12

  g

} # simpleDemoGraph
#----------------------------------------------------------------------------------------------------
test_neo4jMisinterpretedEdges <- function()
{
   message(sprintf("--- test_neo4jMisinterpretedEdges"))
   load("../extdata/neo4jMisinterprtedEdges.RData")
   tbl <- fromJSON(dataFramesToJSON(tbl.edges, tbl.nodes))


} # test_neo4jMisinterpretedEdges
#----------------------------------------------------------------------------------------------------
test_dataFramesToJSON_edgeTableOnly_noExtraAttributes <- function(display)
{
   message(sprintf("--- test_dataFramesToJSON_edgeTableOnly_noExtraAttributes"))

   tbl.edges <- data.frame(source=c("A"),
                           target=c("B"),
                           interaction=c("eats"),
                           stringsAsFactors=FALSE)

   g.json <- dataFramesToJSON(tbl.edges)
   x <- fromJSON(g.json)$elements
   checkEquals(names(x), c("nodes", "edges"))

   tbl.nodes <- x$nodes$data
   checkEquals(dim(tbl.nodes), c(2, 2))
   checkEquals(tbl.nodes$id, c("A", "B"))

   tbl.edges <- x$edges$data
   checkEquals(dim(tbl.edges), c(1, 4))
   checkEquals(colnames(tbl.edges), c("id", "source", "target", "interaction"))
   checkEquals(as.character(tbl.edges[1,]), c("A-(eats)-B", "A", "B", "eats"))

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      Sys.sleep(10)
      browseURL("cyjs-readNetworkFromFile.html")
      } # display


} # test_dataFramesToJSON
#----------------------------------------------------------------------------------------------------
test_dataFramesToJSON_edgeTableOnly_orhpanNodeInNodeTable <- function(display)
{
   message(sprintf("--- test_dataFramesToJSON_edgeTableOnly_orhpanNodeInNodeTable"))

   tbl.edges <- data.frame(source=c("A"),
                           target=c("B"),
                           interaction=c("eats"),
                           stringsAsFactors=FALSE)

   tbl.nodes <- data.frame(id=c("A", "B", "C"),
                           type=c("animal", "vegetable", "mineral"),
                           age=c("recent", "old", "ancient"),
                           stringsAsFactors=FALSE)

   g.json <- dataFramesToJSON(tbl.edges, tbl.nodes)
   x <- fromJSON(g.json)$elements
   checkEquals(names(x), c("nodes", "edges"))

   tbl.nodes <- x$nodes$data
   checkEquals(dim(tbl.nodes), c(3, 3))
   checkEquals(tbl.nodes$id, c("A", "B", "C"))

   tbl.edges <- x$edges$data
   checkEquals(dim(tbl.edges), c(1, 4))
   checkEquals(colnames(tbl.edges), c("id", "source", "target", "interaction"))
   checkEquals(as.character(tbl.edges[1,]), c("A-(eats)-B", "A", "B", "eats"))

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      Sys.sleep(10)
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

}  # test_dataFramesToJSON_edgeTableOnly_orhpanNodeInNodeTable
#----------------------------------------------------------------------------------------------------
test_dataFramesToJSON_edgeTableOnly_addEdgeAttributes <- function(display)
{
   message(sprintf("--- test_dataFramesToJSON_edgeTableOnly_orhpanNodeInNodeTable"))

   tbl.edges <- data.frame(source=c("A"),
                           target=c("B"),
                           interaction=c("eats"),
                           duration="long",
                           intensity=3.2,
                           stringsAsFactors=FALSE)

   g.json <- dataFramesToJSON(tbl.edges)
   x <- fromJSON(g.json)$elements
   checkEquals(names(x), c("nodes", "edges"))

   tbl.nodes <- x$nodes$data
   checkEquals(dim(tbl.nodes), c(2, 2))
   checkEquals(tbl.nodes$id, c("A", "B"))

   tbl.edges <- x$edges$data
   checkEquals(dim(tbl.edges), c(1, 6))
   checkEquals(colnames(tbl.edges), c("id", "source", "target", "interaction", "duration", "intensity"))
   checkEquals(tbl.edges[1, "id"], "A-(eats)-B")
   checkEquals(tbl.edges[1, "source"], "A")
   checkEquals(tbl.edges[1, "target"], "B")
   checkEquals(tbl.edges[1, "duration"], "long")
   checkEquals(tbl.edges[1, "intensity"], 3.2)
   checkEquals(tbl.edges[1, "interaction"], "eats")

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      Sys.sleep(10)
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

}  # test_dataFramesToJSON_edgeTableOnly_addEdgeAttributes
#----------------------------------------------------------------------------------------------------
test_dataFramesToJSON_explicitNodePositions <- function(display)
{
   message(sprintf("--- test_dataFramesToJSON_explicitNodePositions"))

   tbl.nodes <- data.frame(id=c("A", "B", "C"),
                           type=c("kinase", "TF", "glycoprotein"),
                           x=c(0, 100, 200),
                           y=c(200, 100, 0),
                           lfc=c(1, 1, 1),
                           count=c(0, 0, 0),
                           stringsAsFactors=FALSE)

   tbl.edges <- data.frame(source=c("A", "B", "C"),
                           target=c("B", "C", "A"),
                           interaction=c("phosphorylates", "synthetic lethal", "unknown"),
                           stringsAsFactors=FALSE)

   g.json <- dataFramesToJSON(tbl.edges, tbl.nodes)
   x <- fromJSON(g.json)$elements
   checkEquals(names(x), c("nodes", "edges"))
     # make sure the xPos and yPos were translated into
     #   "position": {"x": 0.000000, "y": 200.000000}
     # data members for each node.  this is visible as position.x, position.y colnames
     # of the fromJSON result just above

   checkTrue(all(c("x", "y") %in% colnames(x$nodes$position)))
   checkEquals(x$nodes$position$x, c(0, 100, 200))
   checkEquals(x$nodes$position$y, c(200, 100, 0))

   tbl.nodes <- x$nodes$data
   checkEquals(dim(tbl.nodes), c(3, 6))
   checkEquals(tbl.nodes$id, c("A", "B", "C"))
   checkEquals(colnames(tbl.nodes), c("id", "type", "x", "y", "lfc", "count"))

   tbl.edges <- x$edges$data
   checkEquals(dim(tbl.edges), c(3, 4))
   checkEquals(colnames(tbl.edges), c("id", "source", "target", "interaction"))
   checkEquals(tbl.edges$id, c("A-(phosphorylates)-B", "B-(synthetic lethal)-C", "C-(unknown)-A"))

   if(display){
      writeLines(sprintf("network = %s", g.json), "network.js")
      Sys.sleep(10)
      browseURL("cyjs-readNetworkFromFile.html")
      } # display

}  # test_dataFramesToJSON_explicitNodePositions
#----------------------------------------------------------------------------------------------------
# in early experiments with neo4j, I discovered a bug:  if node ids are not sequentially ordered,
# they break an assumption of the toJSON function.  this test provides a tbl.nodes unordered by id
test_unorderedNodeIDs <- function()
{
   message(sprintf("--- test_unorderedNodeIDs"))

   tbl.nodes <- data.frame(id=c("8","1","2"), label=c("N8", "N1", "N2"), stringsAsFactors=FALSE)
   tbl.edges <- data.frame(id=c(34,23), source=c("8", "2"), target=c("1", "8"),
                           interaction=c("causes", "modifies"), stringsAsFactors=FALSE)
   x <- fromJSON(dataFramesToJSON(tbl.edges, tbl.nodes), simplifyDataFrame=TRUE)
   tbl.e <- x$elements$edges
   tbl.n <- x$elements$nodes

      # fromJSON nests data.frames within the edge and node data.frames
      # not knowing how to fix that, I accomodate that here, reaching
      # deeper into the data structure to make comparisons

      # start by checking the out-of-ascending order N8-causes-N1

   checkEquals(as.character(tbl.e[1,1][, c("source", "target", "interaction")]),
               c("8", "1", "causes"))
   checkEquals(as.character(tbl.e[2,1][, c("source", "target", "interaction")]),
               c("2", "8", "modifies"))

   checkEquals(as.character(tbl.n[1,1]), c("1", "N1"))
   checkEquals(as.character(tbl.n[2,1]), c("2", "N2"))
   checkEquals(as.character(tbl.n[3,1]), c("8", "N8"))

} # test_unorderedNodeIDs
#----------------------------------------------------------------------------------------------------
if(!interactive())
    runTests()