网络-visNetwork包绘制炫酷的动态网络图

visNetwork

visNetwork是一个用于网络可视化的R包，使用的是vis.js javascript库(http://visjs.org)。

visNetwork github : https://github.com/datastorm-open/visNetwork.

#安装visNetwork

install.packages("visNetwork")

# devtools::install_github("datastorm-open/visNetwork") for development version

##查看帮助

# vignette
vignette("Introduction-to-visNetwork")

# full javascript documentation
visDocumentation()

# shiny example
shiny::runApp(system.file("shiny", package = "visNetwork"))

##visNetwork至少需要两个信息:

• 节点，data.frame数据，有id列;
• 边缘，data.frame数据，至少两列，一列起点信息(from)，一列终点信息(to)。

> require(visNetwork, quietly = TRUE)
# minimal example
> nodes <- data.frame(id = 1:3)
id
1
2
3
> edges <- data.frame(from = c(1,2), to = c(1,3))
from to
1  1
2  3
> visNetwork(nodes, edges, width = "100%")

visNetwork

#简单的单个节点和边定制

注：这些设置只是针对单个节点或着边；全局所有点或者节点设置需要使用visNodes 或 visEdges。

##节点属性设置

• label : 指定节点标签的列
• value：指定节点大小
• group：指定节点所属组，igraph包中有许多包装好的方法可以用于网络类群分析
• shape：节点形状，例如circle, square ，triangle
• color：节点颜色
• title：设置提示信息，当您将鼠标悬停在一个节点上时，提示就会出现
• shadow：定义一个节点是否有阴影(TRUE/FALSE)

在node data.frame上添加更多变量。有关可用选项，请参阅visNodes()参数。

visNodes(
  graph,
  id = NULL,
  shape = NULL,
  size = NULL,
  title = NULL,
  value = NULL,
  x = NULL,
  y = NULL,
  label = NULL,
  level = NULL,
  group = NULL,
  hidden = NULL,
  image = NULL,
  mass = NULL,
  physics = NULL,
  borderWidth = NULL,
  borderWidthSelected = NULL,
  brokenImage = NULL,
  labelHighlightBold = NULL,
  color = NULL,
  fixed = NULL,
  font = NULL,
  icon = NULL,
  shadow = NULL,
  scaling = NULL,
  shapeProperties = NULL,
  heightConstraint = NULL,
  widthConstraint = NULL,
  margin = NULL,
  chosen = NULL
)

示例：

> nodes <- data.frame(id = 1:10, 
                    label = paste("Node", 1:10), # add labels on nodes
                    group = c("GrA", "GrB"), # add groups on nodes 
                    value = 1:10, # size adding value
                    shape = c("square", "triangle", "box", "circle", "dot", "star",
                              "ellipse", "database", "text", "diamond"), # control shape of nodes
                    title = paste0("
", 1:10,"
Node !
"), # tooltip (html or character)
                    color = c("darkred", "grey", "orange", "darkblue", "purple"),# color
                    shadow = c(FALSE, TRUE, FALSE, TRUE, TRUE)) # shadow

> head(nodes)
id  label group value    shape                     title    color shadow
1 Node 1   GrA     1   square 
1
Node !
  darkred  FALSE
2 Node 2   GrB     2 triangle 
2
Node !
     grey   TRUE
3 Node 3   GrA     3      box 
3
Node !
   orange  FALSE
4 Node 4   GrB     4   circle 
4
Node !
 darkblue   TRUE
5 Node 5   GrA     5      dot 
5
Node !
   purple   TRUE
6 Node 6   GrB     6     star 
6
Node !
  darkred  FALSE

##边属性设置

• label：指定边标签的列
• title：设置提示信息，当您将鼠标悬停在一个边上时，提示就会出现
• shadow：定义一个节点是否有阴影(TRUE/FALSE)
• length,width：定义网络内边的长度/宽度
• arrows：箭头在边上的位置
• dashes：定义边缘是否应该虚线(TRUE/FALSE)
• smooth：光滑的线(TRUE/FALSE)

在edges data.frame上添加更多变量。有关可用选项，请参阅visEdges()参数。

• 在edge data.frame上添加更多变量。有关可用选项，请参阅visEdges。

visEdges(
  graph,
  title = NULL,
  value = NULL,
  label = NULL,
  length = NULL,
  width = NULL,
  dashes = NULL,
  hidden = NULL,
  hoverWidth = NULL,
  id = NULL,
  physics = NULL,
  selectionWidth = NULL,
  selfReferenceSize = NULL,
  labelHighlightBold = NULL,
  color = NULL,
  font = NULL,
  arrows = NULL,
  arrowStrikethrough = NULL,
  smooth = NULL,
  shadow = NULL,
  scaling = NULL,
  widthConstraint = NULL,
  chosen = NULL
)

示例：

> edges <- data.frame(from = sample(1:10, 8), to = sample(1:10, 8),
                    label = paste("Edge", 1:8), # add labels on edges
                    length = c(100,500), # length
                    arrows = c("to", "from", "middle", "middle;to"), # arrows
                    dashes = c(TRUE, FALSE), # dashes
                    title = paste("Edge", 1:8), # tooltip (html or character)
                    smooth = c(FALSE, TRUE), # smooth
                    shadow = c(FALSE, TRUE, FALSE, TRUE)) # shadow
> head(edges)

##   from to  label length    arrows dashes  title smooth shadow
## 1    4  5 Edge 1    100        to   TRUE Edge 1  FALSE  FALSE
## 2   10  6 Edge 2    500      from  FALSE Edge 2   TRUE   TRUE
## 3    7  8 Edge 3    100    middle   TRUE Edge 3  FALSE  FALSE
## 4    6  4 Edge 4    500 middle;to  FALSE Edge 4   TRUE   TRUE
## 5    3  3 Edge 5    100        to   TRUE Edge 5  FALSE  FALSE
## 6    2  1 Edge 6    500      from  FALSE Edge 6   TRUE   TRUE

visNetwork(nodes, edges, width = "100%")

visNetwork

#全局节点/边配置

• 使用visNodes和visEdges设置节点和边全局属性，并使用visGroups为每个组添加属性。

nodes <- data.frame(id = 1:5, group = c(rep("A", 2), rep("B", 3)))
edges <- data.frame(from = c(2,5,3,3), to = c(1,2,4,2))

visNetwork(nodes, edges, width = "100%") %>% 
  visNodes(shape = "square") %>%                        # square for all nodes
  visEdges(arrows ="to") %>%                            # arrow "to" for all edges
  visGroups(groupname = "A", color = "darkblue") %>%    # darkblue for group "A"
  visGroups(groupname = "B", color = "red")             # red for group "B"

visNetwork

#网络配置

• 网络配置可以使用visOptions, visInteraction, visLayout, visHierarchicalLayout, visPhysics:

##示例数据

> nb <- 10
> nodes <- data.frame(id = 1:nb, label = paste("Label", 1:nb),
 group = sample(LETTERS[1:3], nb, replace = TRUE), value = 1:nb,
 title = paste0("
", 1:nb,"
Tooltip !
"), stringsAsFactors = FALSE)
id   label group value                 title
1 Label 1     A     1 
1
Tooltip !
2 Label 2     C     2 
2
Tooltip !
3 Label 3     C     3 
3
Tooltip !
4 Label 4     A     4 
4
Tooltip !
5 Label 5     A     5 
5
Tooltip !
6 Label 6     B     6 
6
Tooltip !

> edges <- data.frame(from = trunc(runif(nb)*(nb-1))+1,
 to = trunc(runif(nb)*(nb-1))+1,
 value = rnorm(nb, 10), label = paste("Edge", 1:nb),
 title = paste0("
", 1:nb,"
Edge Tooltip !
"))
  from to     value  label                      title
1  6 10.569034 Edge 1 
1
Edge Tooltip !
7  9  9.755302 Edge 2 
2
Edge Tooltip !
4  4 10.618589 Edge 3 
3
Edge Tooltip !
5  4  9.240707 Edge 4 
4
Edge Tooltip !
3  1  8.859133 Edge 5 
5
Edge Tooltip !
4  6 11.003060 Edge 6 
6
Edge Tooltip !

##添加图例

• 你现在可以在节点/边缘上添加更多的自定义图例:

visNetwork(nodes, edges, width = "100%") %>% visLegend()

添加图例

##或传递数据

visNetwork(nodes, edges, width = "100%") %>% 
  visLegend(useGroups = FALSE, addNodes = data.frame(label = "Nodes", shape = "circle"), 
            addEdges = data.frame(label = "link", color = "black"))

passing data

##突出临近点连接（highlight Nearest）

• 使用highlightNearest选项，单击一个节点可以突出显示节点和边:

visNetwork(nodes, edges, width = "100%") %>% 
  visOptions(highlightNearest = TRUE)

highlight Nearest

##可以设置突出程度

visNetwork(nodes, edges, width = "100%") %>% 
  visOptions(highlightNearest = list(enabled =TRUE, degree = 2))

control the degree of depth

##按节点id选择(Select by node id)

你也可以选择节点的id/标签与一个列表与nodesIdSelection:

visNetwork(nodes, edges, width = "100%") %>% 
  visOptions(highlightNearest = TRUE, nodesIdSelection = TRUE)

Select by node id

##通过一列设置选择（Select by a column）

使用selectedBy选项通过列的值选择一些节点:

# can be the column you want
> nodes$sel <- sample(c("sel1", "sel2"), nrow(nodes), replace = TRUE)
id    label group value                  title  sel
1  Label 1     A     1  
1
Tooltip !
 sel1
2  Label 2     C     2  
2
Tooltip !
 sel1
3  Label 3     C     3  
3
Tooltip !
 sel2
4  Label 4     A     4  
4
Tooltip !
 sel2
5  Label 5     A     5  
5
Tooltip !
 sel2
6  Label 6     B     6  
6
Tooltip !
 sel2
7  Label 7     B     7  
7
Tooltip !
 sel1
8  Label 8     C     8  
8
Tooltip !
 sel1
9  Label 9     C     9  
9
Tooltip !
 sel1
10 Label 10     A    10 
10
Tooltip !
 sel2
> visNetwork(nodes, edges, width = "100%") %>%
 visOptions(selectedBy = "sel")

Select by a column

##有向网络

visNetwork(nodes, edges, width = "100%") %>% 
  visEdges(arrows = 'from')

Directed Network

##自定义导航键（Custom navigation）

vis.js提出了一些导航工具:

visNetwork(nodes, edges, width = "100%") %>% 
  visInteraction(navigationButtons = TRUE)

Custom navigation

##数据操作

• 添加一些数据操作工具

visNetwork(nodes, edges, width = "100%") %>% 
  visOptions(manipulation = TRUE)

Data Manipulation

##层次分布

• 可以根据visHierarchicalLayout和visLayout使用和控制分层布局:

nodes <- data.frame(id = 1:7)

edges <- data.frame(
  from = c(1,2,2,2,3,3),
  to = c(2,3,4,5,6,7)
)
visNetwork(nodes, edges, width = "100%") %>% 
  visEdges(arrows = "from") %>% 
  visHierarchicalLayout() 

Hierarchical Layout

# same as   visLayout(hierarchical = TRUE) 

visNetwork(nodes, edges, width = "100%") %>% 
  visEdges(arrows = "from") %>% 
  visHierarchicalLayout(direction = "LR")

Hierarchical Layout

固定网络，不允许缩放

visNetwork(nodes, edges, width = "100%") %>% 
  visInteraction(dragNodes = FALSE, dragView = FALSE, zoomView = FALSE)

Freeze network

##在网络中使用字体图标

• 您可以在组或节点选项使用Font Awesome icons。Font Awesome library (http://fortawesome.github.io/Font-Awesome/)不是依赖的一部分。如果需要，使用addFontAwesome()。

nodes <- data.frame(id = 1:3, group = c("B", "A", "B"))
edges <- data.frame(from = c(1,2), to = c(2,3))

visNetwork(nodes, edges, width = "100%") %>%
  visGroups(groupname = "A", shape = "icon", icon = list(code = "f0c0", size = 75)) %>%
  visGroups(groupname = "B", shape = "icon", icon = list(code = "f007", color = "red")) %>%
  visLegend() %>%
  addFontAwesome()

font awesome icons

#附加特性

##可视化rpart对象

• visTree函数允许可视化和自定义一个rpart分类和回归树。visTreeEditor允许编辑和返回网络，或visTreeModuleServer使用定制树模块。

Visualize rpart object

##在Shiny中使用

• visNetworkOutput 和renderVisNetwork. 在shiny中，可以通过nodesIdSelection选择显示数据。进一步需要实现更多的功能，可以了解visNetworkProxy。

output$mynetwork <- renderVisNetwork({... visOptions(nodesIdSelection = TRUE)}) # created input$mynetwork_selected

And with selectedBy, new input input$mynetwork_selectedBy.

##物理、工具提示、事件

• 可以控制:
• • physics of network : visPhysics
• • events : visEvents

##导出

network <- visNetwork(nodes, edges, width = "100%")
visSave(network, file = "network.html")

##直接使用网络数据(Use DOT language data)

visNetwork(dot = 'dinetwork {1 -> 1 -> 2; 2 -> 3; 2 -- 4; 2 -> 1 }', width = "100%")

DOT language data

##使用gephi json文件

# don't run here
visNetwork(gephi = 'WorldCup2014.json')

#参考：

Itroduction to visNetwork
visNetwork

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