Question

鉴于数据框：

> 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")

我具有以下功能：对权重应用阈值＆＃39;节点，在soi和all_nodes变量的节点之间给出不同的节点颜色，最后绘制图形。

现在的情况是，正如您所看到的，阈值应用于所有节点＆＃39;权重，无论它们属于哪个集合（soi OR all_nodes）。结果是从图中删除属于soi集的顶点，这是我不想要的。

实际上，我想绘制所有属于soi集的顶点并使用threshold过滤掉那些不属于soi的{{1}}的顶点setdiff(all_nodes,soi)。

这是功能。

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)

并且在最终的绘图节点中，G属于soi时不会出现。{/ p>

有没有办法不过滤soi个节点？

Answer 1

要保留所有soi个节点，您只需要为delete.vertices调用添加一些逻辑：

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)

}

在特定顶点上应用阈值＆＃39;重量

1 个答案: