cyRESTを使って緑の毛玉を描く

実行に必要なもの
Cytoscape 3.1以上
cyREST(CytoscapeのApp)

実行前の準備
cyRESTを追加したCytoscapeを起動しておくこと

# 1. graphオブジェクト準備 
library(igraph)
g <- static.power.law.game(no.of.nodes=10000, no.of.edges=30000, 2.3, 2.4)
V(g)$degree <- degree(g) # 次数(ノードに接するエッジの数)

# 2. graph → JSON 変換
library(RJSONIO)
library(httr)
devtools::source_url("https://raw.githubusercontent.com/idekerlab/cy-rest-R/develop/toCytoscape.R")
cygraph <- toCytoscape(g)

# 3. JSONデータ送信
res <- POST(url="http://localhost:1234/v1/networks", body=cygraph, encode="json")
network.suid <- unname(fromJSON(rawToChar(res$content)))

この時点でCytoscaopeに何も表示されていない場合は下記コードを実行する

POST(paste("http://localhost:1234/v1/networks/", toString(network.suid), "/views", sep=""))

続き

# 4. レイアウト変更
GET(paste("http://localhost:1234/v1/apply/layouts/force-directed/", toString(network.suid), sep=""))

この処理の後、レイアウトが変わらない時はCytoscapeで時点でレイアウトOrganicを行う

続き

# 6. スタイル作成
style.name = "midorinokedama"

# デフォルト
def.background.color <- list(
  visualProperty = "NETWORK_BACKGROUND_PAINT",
  value = "#000000"
)

# Node
def.node.color <- list(
  visualProperty = "NODE_FILL_COLOR",
  value = "#00FF00"
)
def.node.label <- list(
  visualProperty = "NODE_LABEL",
  value = ""
)
def.node.borderwidth <- list(
  visualProperty = "NODE_BORDER_WIDTH",
  value = 0.0
)
def.node.transparency <- list(
  visualProperty = "NODE_TRANSPARENCY",
  value = 150
)
def.node.shape <- list(
  visualProperty = "NODE_SHAPE",
  value = "ELLIPSE"
)

# Edge
def.edge.color <- list(
  visualProperty = "EDGE_STROKE_UNSELECTED_PAINT",
  value = "#00FF00"
)
def.edge.transparency <- list(
  visualProperty = "EDGE_TRANSPARENCY",
  value = 80
)
def.edge.width <- list(
  visualProperty = "EDGE_WIDTH",
  value = 2.0
)

defaults <- list(
  def.background.color,
  def.node.color, 
  def.node.label,
  def.node.borderwidth,
  def.node.transparency, 
  def.edge.color, 
  def.edge.transparency, 
  def.edge.width
)

# マッピング
min.degree = min(V(g)$degree)
max.degree = max(V(g)$degree)

# ノードの大きさ
ns.point1 = list(
  value=min.degree,
  lesser= "1.0",
  equal="2.0",
  greater="2.0"
)

ns.point2 = list(
  value=max.degree,
  lesser="150.0",
  equal="150.0",
  greater="1.0"
)

node.size.continuous.points = list(ns.point1, ns.point2)

node.size = list(
  mappingType="continuous",
  mappingColumn="degree",
  mappingColumnType="Double",
  visualProperty="NODE_SIZE",
  points = node.size.continuous.points
)

# ノードの色
nc.point1 = list(
  value=5.0,
  lesser= "#00FF00",
  equal="#00FF00",
  greater="#00FF00"
)

nc.point2 = list(
  value=10,
  lesser="#FFFFFF",
  equal="#FFFFFF",
  greater="#FFFFFF"
)

node.color.continuous.points = list(nc.point1, nc.point2)

node.color = list(
  mappingType="continuous",
  mappingColumn="degree",
  mappingColumnType="Double",
  visualProperty="NODE_FILL_COLOR",
  points = node.color.continuous.points
)

mappings = list(node.size, node.color)

style <- list(title = style.name, defaults = defaults, mappings = mappings)
style.JSON <- toJSON(style)
POST(url="http://localhost:1234/v1/styles", body=style.JSON, encode = "json")
GET(paste("http://localhost:1234/v1/apply/styles/midorinokedama/", toString(network.suid), sep=""))

Enjoy!

cyRESTを使って緑の毛玉を描く

Saturday, February 21, 2015