网络-networkD3 绘制动态网络

image.png

可视化数据时，网络可以很好展示各个节点之间的关系以及关系的重要性。网络中存在大量的节点和边，因此绘制一个好的网络会有助于信息的解读。networkD3可以自定义网络的各种特征，绘制一个优美的动态网络。

#1. 安装

install.packages("networkD3")

#2. 使用

networkD3 绘图基于JavaScript，所以索引是从0开始的；R中从1开始。

可以使用R包 igraph构建网络绘制需要的数据，使用igraph_to_networkD3函数将数据转换成networkD3 要求格式的输入数据。

##2.1 simpleNetwork

simpleNetwork(Data, Source = 1, Target = 2, height = NULL, width = NULL,
  linkDistance = 50, charge = -30, fontSize = 7, fontFamily = "serif",
  linkColour = "#666", nodeColour = "#3182bd", opacity = 0.6, zoom = F)

simpleNetwork是networkD3的基础函数，可以快速出图。

绘制网络

# Load package
library(networkD3)

# Create fake data
src <- c("A", "A", "A", "A",
        "B", "B", "C", "C", "D")
target <- c("B", "C", "D", "J",
            "E", "F", "G", "H", "I")
networkData <- data.frame(src, target)

# Plot
simpleNetwork(networkData)

simpleNetwork

##2.2 forceNetwork

forceNetwork有更多的参数，调整参数可以绘制更复杂的网络图。

forceNetwork(Links, Nodes, Source, Target, Value, NodeID, Nodesize, Group,
  height = NULL, width = NULL,
  colourScale = JS("d3.scaleOrdinal(d3.schemeCategory20);"), fontSize = 7,
  fontFamily = "serif", linkDistance = 50,
  linkWidth = JS("function(d) { return Math.sqrt(d.value); }"),
  radiusCalculation = JS(" Math.sqrt(d.nodesize)+6"), charge = -30,
  linkColour = "#666", opacity = 0.6, zoom = FALSE, legend = FALSE,
  arrows = FALSE, bounded = FALSE, opacityNoHover = 0,
  clickAction = NULL)

Links：边的数据集
Nodes：节点数据集
Source：边的数据集中列名，指定边起始点
Target：边的数据集中列名，指定边终点
Value：边宽度的数据，一般时边权重
NodeID：节点数据集中节点的列
Nodesize：节点大小
Group：节点的分组
height = NULL：网络高度
width = NULL：网络宽度
fontFamily = "serif"：字体
linkColour = "#666"：边的颜色
opacity = 0.6：节点透明度
zoom = FALSE：图是否可以缩放
legend = FALSE：是否展示图例
arrows = FALSE：边是否有箭头
bounded = FALSE：图是否显示边界
opacityNoHover = 0：鼠标选择某个节点时，其他节点的透明度
clickAction = NULL：JavaScript语言表达式，定义当节点被点击时，需要的操作

绘制网络
forceNetwork的数据格式比较麻烦； 尤其是参数Nodes；建议大家使用igraph包 igraph_to_networkD3()网络图所需数据将转换为networkD3数据格式。本文见#3. 与igraph交互部分。

# Create fake data
src <- c("A", "A", "A", "A",
         "B", "B", "C", "C", "D")
target <- c("B", "C", "D", "J",
            "E", "F", "G", "H", "I")
networkData <- data.frame(src, target)

nodeData <- data.frame(name=unique(c(src, target)),
                       group= c(rep(1,5),rep(2,5)))
linkData <- data.frame(source = (match(networkData$src, nodeData$name)-1),
                       target = (match(networkData$target, nodeData$name)-1),
                       value = rnorm(length(src), mean=0, sd=1))
forceNetwork(
  Links = linkData,
  Nodes = nodeData,
  Source = "source",
  Target = "target",
  Value = "value",
  NodeID = "name",Group = "group")

forceNetwork by self

# Load data
data(MisLinks)
data(MisNodes)

# Plot
forceNetwork(Links = MisLinks, Nodes = MisNodes,
            Source = "source", Target = "target",
            Value = "value", NodeID = "name",
            Group = "group", opacity = 0.8)

image.png

# with a simple click action - make the circles bigger when clicked
MyClickScript <- 
  '      d3.select(this).select("circle").transition()
.duration(750)
.attr("r", 30)'

forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
             Target = "target", Value = "value", NodeID = "name",
             Group = "group", opacity = 1, zoom = F, bounded = T,
             clickAction = MyClickScript)

image.png

MyClickScript <- 'alert("You clicked " + d.name + " which is in row " + (d.index + 1) +
" of your original R data frame");'
forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
             Target = "target", Value = "value", NodeID = "name",
             Group = "group", opacity = 1, zoom = F, bounded = T,
             clickAction = MyClickScript)

image.png

# Create graph with legend and varying radius
forceNetwork(Links = MisLinks, Nodes = MisNodes, Source = "source",
             Target = "target", Value = "value", NodeID = "name",
             Nodesize = 'size', radiusCalculation = "d.nodesize",
             Group = "group", opacity = 1, legend = T, bounded = F) 

image.png

##2.3 桑基图

# Load energy projection data
URL <- paste0(
        "https://cdn.rawgit.com/christophergandrud/networkD3/",
        "master/JSONdata/energy.json")
Energy <- jsonlite::fromJSON(URL)
# Plot
sankeyNetwork(Links = Energy$links, Nodes = Energy$nodes, Source = "source",
             Target = "target", Value = "value", NodeID = "name",
             units = "TWh", fontSize = 12, nodeWidth = 30)

sankeyNetwork

##2.4 放射状网络

URL <- paste0(
        "https://cdn.rawgit.com/christophergandrud/networkD3/",
        "master/JSONdata//flare.json")

## Convert to list format
Flare <- jsonlite::fromJSON(URL, simplifyDataFrame = FALSE)

# Use subset of data for more readable diagram
Flare$children = Flare$children[1:3]

radialNetwork(List = Flare, fontSize = 10, opacity = 0.9)

radialNetwork

diagonalNetwork(List = Flare, fontSize = 10, opacity = 0.9)

diagonalNetwork

##2.5 树状图

hc <- hclust(dist(USArrests), "ave")

dendroNetwork(hc, height = 600)

dendroNetwork

#3. 与igraph交互

调用 igraph 包创建网络图所需数据，igraph_to_networkD3函数转换数据格式，networkD3绘制图。

# Load igraph
library(igraph)

# Use igraph to make the graph and find membership
karate <- make_graph("Zachary")
wc <- cluster_walktrap(karate)
members <- membership(wc)

# Convert to object suitable for networkD3
karate_d3 <- igraph_to_networkD3(karate, group = members)

# Create force directed network plot
forceNetwork(Links = karate_d3$links, Nodes = karate_d3$nodes, 
             Source = 'source', Target = 'target', 
             NodeID = 'name', Group = 'group')

forceNetwork

#4. 动态网络图输出

##4.1 保存成HTML

library(magrittr)

simpleNetwork(networkData) %>%
saveNetwork(file = 'Net1.html')

##4.2 内置于RMarkdown

参考networkD3

##4.3 内置于Shiny

在server.R调用render*Network（*可以是 Simple,Force, Sankey）

output$force <- renderForceNetwork({
forceNetwork(Links = MisLinks, Nodes = MisNodes,
            Source = "source", Target = "target",
            Value = "value", NodeID = "name",
            Group = "group", opacity = input$opacity)
})

在app.R文件中调用*NetworkOutput（*可以是 Simple,Force, Sankey）

forceNetworkOutput("force")

shiny例子：networkD3-shiny-example

shiny::runGitHub('christophergandrud/networkD3-shiny-example')

#5. 参考：

networkD3 :D3 JavaScript Network Graphs from R
networkD3 github

系列文章：
R语言进行网络分析的基础包 igraph
networkD3 绘制动态网络
网络-visNetwork包绘制炫酷的动态网络图
网络-调用R包构建交互式网络可视化的Shiny App