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对特定顶点的权重应用阈值

igraph filter plot r

J. Doe · 技术社区 · 6 年前

给定数据帧:

> dput(rel.matrix)
structure(list(from = c("A", "A", "A", "A", "B", "B", "B", "B", 
"C", "C", "C", "C", "C", "C", "D", "D", "D", "D", "E", "E", "E", 
"E", "F", "F", "F", "F", "F", "F", "G", "G", "G", "G", "H", "H", 
"H", "H", "I", "I", "I", "I", "J", "J", "J", "J", "K", "K"), 
    to = c("B", "C", "D", "E", "A", "C", "D", "E", "A", "B", 
    "D", "E", "F", "K", "A", "B", "C", "E", "A", "B", "C", "D", 
    "C", "G", "H", "I", "J", "K", "F", "H", "I", "J", "F", "G", 
    "I", "J", "F", "G", "H", "J", "F", "G", "H", "I", "C", "F"
    ), weight = c(0.09137056, 0.2677665, 0.09137056, 0.09137056, 
    0.09137056, 0.09517766, 0.02284264, 0.02284264, 0.2677665, 
    0.09517766, 0.09517766, 0.09517766, 0.3730964, 0.1675127, 
    0.09137056, 0.02284264, 0.09517766, 0.02284264, 0.09137056, 
    0.02284264, 0.09517766, 0.02284264, 0.3730964, 0.09517766, 
    0.09517766, 0.2677665, 0.09517766, 0.1675127, 0.09517766, 
    0.02284264, 0.09137056, 0.02284264, 0.09517766, 0.02284264, 
    0.09137056, 0.02284264, 0.2677665, 0.09137056, 0.09137056, 
    0.09137056, 0.09517766, 0.02284264, 0.02284264, 0.09137056, 
    0.1675127, 0.1675127)), row.names = c(NA, -46L), class = "data.frame")

和两组节点

> dput(soi)
c("A", "I", "G")
> dput(all_nodes)
c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K")

我有以下函数,在权重的节点上应用一个阈值,在 soi 和 all_nodes 变量,最后绘制出图表。

现在的情况是,正如您所看到的,阈值应用于所有节点的权重,而不考虑设置( soi公司 或 所有\u节点 )它们属于。其结果是从绘图中删除属于 soi公司 这是我不想要的。

实际上,我想画出所有属于 soi公司 使用设置和筛选 threshold 只有那些不属于 soi公司 哪些是 setdiff(all_nodes,soi) 。

下面是函数。

graph_rel_network <- function ( rel.matrix, nodes.names, soi.names, threshold )
{
  # setup vertices meta data which contain soi and not soi
  meta <- cbind( nodes.names, issoi = nodes.names %in% soi.names )

  # read in a graph: the weights are in the edge attributes
  g <- igraph::graph_from_data_frame(rel.matrix, directed = TRUE, vertices =  meta)
  g <- as.undirected(g, mode = "collapse")
  # rescale weights
  E(g)$weight2 <- 9 * E(g)$weight / max(E(g)$weight)

  # remove edges acoarding to the threshold
  g_sub <- delete.edges(g, E(g)[weight2 <= threshold ])

  # remove vertices with 0 degree
  g_sub <- delete.vertices(simplify(g_sub), degree(g_sub)==0)

  # color vertices that belongs to soi
  V(g_sub)$color <- ifelse(V(g_sub)$issoi == TRUE, "gold", "tomato")

  # plot the graph
  plot.igraph( g_sub,
               edge.width=E(g_sub)$weight2,
               vertex.label.dist=0,
               vertex.frame.color="gray",
               vertex.label.color="black")

  legend(x=-1.5, y=-1.1,
         c("Nodes of interest","Most Relevant nodes"),
         pch=21,
         pt.bg= c('gold','tomato'),
         pt.cex=2,
         cex=1,
         bty="n",
         ncol=1)

}

例如,您可以执行 graph_rel_network( rel.matrix, all_nodes, soi, 3)

在最后一个绘图节点中, G 当它属于时不会出现 soi公司 。

有没有办法不过滤 soi公司 节点?

1 回复 | 直到 6 年前

emilliman5 6 年前

保留所有 soi 节点只需向 delete.vertices 电话:

graph_rel_network <- function (rel.matrix, nodes.names, soi.names, threshold )
{
  # setup vertices meta data which contain soi and not soi
  ###changed meta to a data.frame so that issoi is stored as logical instead of character
  meta <- data.frame(nodes.names, issoi = nodes.names %in% soi.names )  
  # read in a graph: the weights are in the edge attributes
  g <- igraph::graph_from_data_frame(rel.matrix, directed = TRUE, vertices =  meta)
  g <- as.undirected(g, mode = "collapse")

  # rescale weights
  E(g)$weight2 <- 9 * E(g)$weight / max(E(g)$weight)

  ###Create a subnetwork of soi nodes only
  g_soi  <- induced_subgraph(g, vids = V(g)[V(g)$name %in% soi.names])
  # remove edges acoarding to the threshold
  g_sub <- delete.edges(g, E(g)[E(g)$weight2 <= threshold])

  # remove vertices with 0 degree
  g_sub <- delete.vertices(g_sub, (degree(g_sub)==0 & !V(g)$issoi))

  ###Merge the tresholded allnode network with the soi network
  g_merge <- union(g_sub, g_soi)

  ###Resolve some attribute naming conflicts from the merge
  E(g_merge)$weight2 <- colMeans(rbind(E(g_merge)$weight2_2, E(g_merge)$weight2_1), na.rm = T)
  # color vertices that belongs to soi
  V(g_merge)$color <- ifelse(V(g_merge)$issoi_1, "gold", "tomato")

  # plot the graph
  plot.igraph( g_merge,
               edge.width=E(g_merge)$weight2,
               vertex.label.dist=0,
               vertex.frame.color="gray",
               vertex.label.color="black")

  legend(x=-1.5, y=-1.1,
         c("Nodes of interest","Most Relevant nodes"),
         pch=21,
         pt.bg= c('gold','tomato'),
         pt.cex=2,
         cex=1,
         bty="n",
         ncol=1)

}