为什么igraph图警告“要替换的项目数不是替换长度的倍数"? [英] Why igraph plot warns that "number of items to replace is not a multiple of replacement length"?

问题描述

我有一个在两个节点之间有很多边的图.当我绘制它时，我会收到一条警告，在这种情况下我不理解.

I have a graph with many edges between two nodes. When I plot it, I get a warning I don't understand in this context.

这很好:

library(igraph)
gg <- graph.empty(n=0, directed=TRUE)
gg <- gg + vertex("10501")
gg <- gg + edge("10501", "10501")
gg <- gg + edge("10501", "10501")
plot(gg)

但是同一条带有更多边的图形会发出警告:

But the same graph with one more edge gives a warning:

gg <- graph.empty(n=0, directed=TRUE)
gg <- gg + vertex("10501")
gg <- gg + edge("10501", "10501")
gg <- gg + edge("10501", "10501")
gg <- gg + edge("10501", "10501")
plot(gg)

我看不出原因.为什么会有这个警告?

I fail to see the reason. Why this warning?

推荐答案

在igraph包源中搜索给出警告的行，看来罪魁祸首功能是plot.common.R中的autocurve.edges:

Searching the igraph package source for the line giving the warning, it seems that the culprit function is autocurve.edges in plot.common.R:

autocurve.edges <- function(graph, start=0.5) {
  cm <- count.multiple(graph)
  el <- apply(get.edgelist(graph, names=FALSE), 1, paste, collapse=":")
  ord <- order(el)
  res <- numeric(length(ord))

  p <- 1
  while (p <= length(res)) {
    m <- cm[ord[p]]
    idx <- p:(p+m-1)
    if (m==1) {
      r <- 0
    } else {
      r <- seq(-start, start, length=m)
    }
    res[ord[idx]] <- r
    p <- p + m
  }
  res
}

根据?igraph.plotting(和程序包的源代码)，默认情况下将调用autocurve.edges函数来确定如何弯曲边缘:

According to ?igraph.plotting (and the package source) the autocurve.edges function is the called by default to determine how to curve edges:

默认情况下，指定曲线的矢量是通过调用autocurve.edges函数来计算的.此功能可确保多个边缘是弯曲的并且全部可见.对于循环边缘，将忽略此参数.

By default the vector specifying the curvatire is calculated via a call to the autocurve.edges function. This function makes sure that multiple edges are curved and are all visible. This parameter is ignored for loop edges.

从igraph.plot的早期开始，我们可以看到此函数被调用，并传递了整个图形:

From early in igraph.plot, we can see that this function is called, being passed the whole graph:

curved             <- params("edge", "curved")
if (is.function(curved)) { curved <- curved(graph) }

这是问题图形上警告的来源:

This is the source of the warnings on the problematic graph:

autocurve.edges(gg)
# [1] -0.5 -0.5  0.0
# Warning messages:
# 1: In res[ord[idx]] <- r :
#   number of items to replace is not a multiple of replacement length
# 2: In res[ord[idx]] <- r :
#   number of items to replace is not a multiple of replacement length

要深入研究为什么会看到这些问题，此函数要做的第一件事是调用count.multiple，该函数返回每个边重复的次数.在有问题的图中:

To delve into why we're seeing these issues, the very first thing this function does is call count.multiple, which returns the number of times each edge is repeated. In the offending graph:

count.multiple(gg)
# [1] 1.5 1.5 1.5

而不是返回c(3, 3, 3)(因为循环边重复了3次)，而是返回了c(1.5, 1.5, 1.5).尽管在?count.multiple中我没有看到任何有关此的信息，但是发生这种情况的原因是，如果边缘是循环的(即从节点到其自身的边缘)，则边缘的计数将除以2，这是由于以下行中的igraph_count_multiple程序包源中structural_properties.c文件中的igraph_count_multiple:

Instead of returning c(3, 3, 3) (since the looping edge is repeated 3 times), it's returning c(1.5, 1.5, 1.5). Though I don't see any mention of this in ?count.multiple, this is happening because the count of an edge is divided by 2 if it is a loop (aka an edge from a node to itself), due to the following line in igraph_count_multiple from the structural_properties.c file in the igraph package source:

/* for loop edges, divide the result by two */
if (to == from) VECTOR(*res)[i] /= 2;

生成警告的事实是由于存在错误-autocurve.edges预期会获得c(3, 3, 3)，但由于循环边缘而从count.multiple获得了c(1.5, 1.5, 1.5).我认为autocurve.edges实际上可以使用类似以下的方式在纯R中重新实现:

The fact that the warnings are generated is due to a bug -- autocurve.edges was expecting to get c(3, 3, 3) but instead got c(1.5, 1.5, 1.5) from count.multiple due to the loop edges. I think autocurve.edges could actually be reimplemented in pure R using something like:

autocurve.edges <- function(graph, start=0.5) {
  el <- apply(get.edgelist(graph, names=FALSE), 1, paste, collapse=":")
  ave(rep(NA, length(el)), el, FUN=function(x) {
    if (length(x) == 1) {
      return(0)
    } else {
      return(seq(-start, start, length=length(x)))
    }
  })
}

此外，我认为count.multiple的文档应该进行更新，以提及其对循环边的特殊处理.

Further, I think the documentation of count.multiple should be updated to mention its special handling of loop edges.

同时，我认为您的解决方案是手动指定曲率参数以避免出现警告:

In the meantime, I think the solution in your case would be to manually specify your curvature parameter to avoid the warnings:

plot(gg, edge.curved=FALSE)

更新:作为拉取请求提交给rigraph项目，现在合并到R igraph项目的dev分支中:

Update: Submitted as a pull request to the rigraph project and now merged into the dev branch of the R igraph project: https://github.com/igraph/rigraph/pull/80

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