Question

我试图在我自己的data.frames中使用example code here for doing iGraph network graphs in plotly和鞋拔，而不是使用示例空手道俱乐部数据。绘制图形时，似乎忽略了边缘列表，并且正在建立一堆随机连接。我认为标签或边缘都是错误的，但我不能说。

library(igraph)
library(plotly)

setwd('C:/Users/Andrew Riffle/Documents/MEGAsync/code/R/link_analysis')

ID <- c(1:50)
nodes <- data.frame(ID)

Source <- c(23, 24, 36, 20, 36, 41, 12, 8, 18, 28)
Target <- c(5, 7, 9, 35, 23, 12, 38, 29, 33, 45)
links <- data.frame(Source, Target)

net <- graph_from_data_frame(d=links, vertices=nodes, directed=FALSE)

net <- simplify(net, remove.multiple = F, remove.loops = T)

tkplot(net, vertex.label=nodes$id, vertex.label.color='white', layout=layout.fruchterman.reingold)

#####Begin plotly example code unmodified unless commented#####

G <- upgrade_graph(net) #put my iGraph object instead of the karate club one
L <- layout.circle(G)

vs <- V(G)
es <- as.data.frame(get.edgelist(G))

Nv <- length(vs)
Ne <- length(es[1]$V1)

Xn <- L[,1]
Yn <- L[,2]

network <- plot_ly(x = ~Xn, y = ~Yn, mode = "markers", text = vs$name, hoverinfo = "text")

edge_shapes <- list()
for(i in 1:Ne) {
  v0 <- es[i,]$V1
  v1 <- es[i,]$V2

  edge_shape = list(
    type = "line",
    line = list(color = "#030303", width = 0.3),
    x0 = Xn[v0],
    y0 = Yn[v0],
    x1 = Xn[v1],
    y1 = Yn[v1]
  )

  edge_shapes[[i]] <- edge_shape
}

axis <- list(title = "", showgrid = FALSE, showticklabels = FALSE, zeroline = FALSE)

p <- layout(
  network,
  title = 'Test Network', #Changed the title
  shapes = edge_shapes,
  xaxis = axis,
  yaxis = axis
)

p #added a call to display p instead of upload to plot.ly

当我运行时，我得到this nice pretty iGraph that has been plotted by Plotly。但是，边缘不正确。似乎只有ID的1-10连接，而且只有其他ID小于10.这些连接都不在边缘列表中，如下所示。

   Source Target
1      24     35
2      12     23
3      41     12
4      23      7
5      18      5
6      20      9
7      28     29
8      36     45
9       8     33
10     36     38

有谁看到我做错了什么？帮助赞赏。

Answer 1

发现该教程实际上是错误的。如果使用plot与使用plotly相比，使用plot绘制相同的空手道网络，plotly中的许多连接都不在clipToPadding=false中。

我已经放弃了尝试做这项工作，visNetwork是一个很好的选择，我已经更容易搞清楚了。建议任何有类似问题的人阅读本文。

Answer 2

我知道对于OP来说有点太晚了，但对于其他偶然发现同样问题的人（就像我一样）。

我可以在教程源代码中建议以下五个更改：

G <- upgrade_graph(net)
L <- layout.circle(G)
rownames(L) <- get.vertex.attribute(G)$name           #added line (#1 out of 5)

vs <- V(G)
es <- as.data.frame(get.edgelist(G))

Nv <- length(vs)
Ne <- length(es[1]$V1)

Xn <- L[,1]
Yn <- L[,2]

network <- plot_ly(x = ~Xn, y = ~Yn, mode = "markers", text = vs$name, hoverinfo = "text")

edge_shapes <- list()
for(i in 1:Ne) {
  v0 <- es[i,]$V1
  v1 <- es[i,]$V2

  edge_shape = list(
    type = "line",
    line = list(color = "#030303", width = 0.3),
    x0 = L[which(v0==rownames(L)),][1],               #changed line (#2 out of 5)                
    y0 = L[which(v0==rownames(L)),][2],               #changed line (#3 out of 5)
    x1 = L[which(v1==rownames(L)),][1],               #changed line (#4 out of 5)
    y1 = L[which(v1==rownames(L)),][2]                #changed line (#5 out of 5)
  )

  edge_shapes[[i]] <- edge_shape
}

axis <- list(title = "", showgrid = FALSE, showticklabels = FALSE, zeroline = FALSE)

p <- layout(
  network,
  title = 'Test Network', #Changed the title
  shapes = edge_shapes,
  xaxis = axis,
  yaxis = axis
)

p

现在工作正常。

iGraph + Plotly创建随机连接

2 个答案: