节点不尊重 ggraph/igraph 中的刻面

Question

我在理解ggplot2 和ggraph 在刻面方面的区别时遇到了一些麻烦。考虑以下数据：

library(igraph)
library(ggraph)
library(ggplot2)

df <- structure(list(x = c("H001", "H024", "H090", "H090", "H098", 
                     "H103", "H126", "H152", "H155", "H155", "B002", "B011", "B075", 
                     "B092", "M002", "M002", "M002", "M050", "M050", "M085", "M085", 
                     "M247", "M247", "M247"), 
               y = c("H103", "H126", "H152", "H155","H155", "H001", "H024", "H090", "H090", "H098", "B092", "B075", 
                      "B011", "B002", "M050", "M085", "M247", "M002", "M247", "M002", "M247", "M002", "M050", "M085"), 
               r = c(0.963248925980302, 0.991452643542894, 0.965947578382865, 
                     0.963234153063794, 0.962277411462605, 0.963248925980302, 
                     0.991452643542894, 0.965947578382865, 0.963234153063794, 
                     0.962277411462605, 0.960948147492217, 0.957371360458182, 
                     0.957371360458182, 0.960948147492217, 0.96976135236222, 
                     0.977435712803837, 0.997037031981303, 0.96976135236222, 
                     0.978553503235858, 0.977435712803837, 0.992741796542001, 
                     0.997037031981303, 0.978553503235858, 0.992741796542001), 
               facet_var = c("08MH", "08MH", "08MH", "08MH", "08MH", "08MH", "08MH", "08MH", "08MH", 
                             "08MH", "08HB", "08HB", "08HB", "08HB", "08NM", "08NM", "08NM", "08NM", 
                             "08NM", "08NM", "08NM", "08NM", "08NM", "08NM")), 
          class = "data.frame", row.names = c(NA, -24L), .Names = c("x", "y", "r", "facet_var")
)

如果我使用简单的 ggplot 绘制数据，我可以以一种我认为“正常”的方式进行刻面：

ggplot(df, aes(x = x, y = y)) +
         geom_point() +
         facet_wrap(~facet_var)

也就是说facet_var 的每个级别都有一些与之关联的点，并且只有这些点被绘制在相应的方面。现在，如果我使用ggraph 尝试类似的方法，我会遇到对我来说很奇怪的行为（尽管我显然承认它只是反映了缺乏理解）：

graph_cors <- graph_from_data_frame(df, directed = FALSE)

ggraph(graph_cors) +
  geom_edge_link(aes(edge_alpha = abs(r), color = r), edge_width = 2) +
  guides(edge_alpha = "none") +
  scale_edge_colour_gradientn(limits = c(-1, 1), colors = topo.colors(5)) +
  geom_node_point(color = "black", size = 5) +
  geom_node_text(aes(label = name), repel = TRUE) +
  facet_edges(~facet_var)

因此，尽管边缘尊重刻面，但所有节点都绘制在每个刻面中。谁能在这里概述我做错了什么？

会话信息

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Canada.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggraph_1.0.0    ggplot2_2.2.1   igraph_1.1.2    testthat_1.0.2  devtools_1.13.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13          compiler_3.4.2        plyr_1.8.4            bindr_0.1             viridis_0.4.0        
 [6] tools_3.4.2           digest_0.6.12         viridisLite_0.2.0     memoise_1.1.0         tibble_1.3.4         
[11] gtable_0.2.0          pkgconfig_2.0.1       rlang_0.1.2           rstudioapi_0.7.0-9000 ggrepel_0.7.0        
[16] yaml_2.1.14           bindrcpp_0.2          gridExtra_2.3         withr_2.0.0           dplyr_0.7.4          
[21] grid_3.4.2            glue_1.1.1            R6_2.2.2              tweenr_0.1.5          udunits2_0.13        
[26] magrittr_1.5          scales_0.5.0          fortunes_1.5-4        MASS_7.3-47           units_0.4-6          
[31] assertthat_0.2.0      swtext_0.0.1          ggforce_0.1.1         colorspace_1.3-2      lazyeval_0.2.0       
[36] munsell_0.4.3         crayon_1.3.4    

Answer 1

您需要将相关变量作为节点属性分配给按节点分面。您的 facet_var 变量是一个边缘属性；如果您将其分配给每个 dyad 中的每个节点作为节点属性，则 faceting 有效。

facet_graph 由 两个 变量（例如边缘属性和节点属性）组成的构面。似乎facet_nodes 是您想要的，但您需要将节点属性发送到参数，而不是边缘属性。

目前，您的igraph 对象只有一个边缘属性：

> graph_cors
IGRAPH UN-- 16 24 -- 
+ attr: name (v/c), r (e/n), facet_var (e/c)
+ edges (vertex names):
 [1] H001--H103 H024--H126 H090--H152 H090--H155 H098--H155 H001--H103 H024--H126 H090--H152
 [9] H090--H155 H098--H155 B002--B092 B011--B075 B011--B075 B002--B092 M002--M050 M002--M085
[17] M002--M247 M002--M050 M050--M247 M002--M085 M085--M247 M002--M247 M050--M247 M085--M247

graph_cors <- graph_from_data_frame(df, directed = FALSE)

facet_nodes <- cbind(c(df[,1], df[,2]), 
                     df[match(c(df[,1], df[,2]), df[,1]),4])

# Assign the facet_var variable to corresponding dyad pairs
V(graph_cors)$facet_node <- facet_nodes[match(V(graph_cors)$name, facet_nodes[,1]),2]

现在，igraph 对象有一个节点属性（“facet_node”）：

> graph_cors
IGRAPH UN-- 16 24 -- 
+ attr: name (v/c), facet_node (v/c), r (e/n), facet_var (e/c)
+ edges (vertex names):
 [1] H001--H103 H024--H126 H090--H152 H090--H155 H098--H155 H001--H103 H024--H126 H090--H152
 [9] H090--H155 H098--H155 B002--B092 B011--B075 B011--B075 B002--B092 M002--M050 M002--M085
[17] M002--M247 M002--M050 M050--M247 M002--M085 M085--M247 M002--M247 M050--M247 M085--M247

# Use the facet_nodes argument with the nodal attribute
ggraph(graph_cors) +
  geom_edge_link(aes(edge_alpha = abs(r), color = r), edge_width = 2) +
  guides(edge_alpha = "none") +
  scale_edge_colour_gradientn(limits = c(-1, 1), colors = topo.colors(5)) +
  geom_node_point(color = "black", size = 5) +
  geom_node_text(aes(label = name), repel = TRUE) +
  facet_nodes(~facet_node)

Answer 2

我认为这是设计使然，您没有做任何“错误”的事情。

facet_edges 在每个面板中重复节点并绘制映射到变量的边。

facet_nodes 绘制映射到变量的节点并绘制面板中存在终端节点的边。

facet_graph - 来自其文档 - “处理所有这些问题，允许您定义行和列引用的数据类型以及根据每个面板中的节点过滤边缘（即使节点未绘制）。”

所以facet_nodes 或facet_graph 的行为可能更符合您的预期。