尝试使用ggraph
包绘制网络并指定每个节点的坐标。虽然我可以使用igraph
包实现此功能 - 但我无法使用ggraph
包执行此操作。
# reproducible example to generate a random graph
library(igraph)
g1 <- erdos.renyi.game(20, 1/2)
plot(g1)
# function to produce coordinates for each node in order of the node
# degree (number of links per node)
coord <- function(g){
n.nod <- length(V(g))
mat.c <- matrix(0, nrow = n.nod, ncol = 2)
deg <- degree(g)
uniq.deg <- unique(deg)
min.d <- min(deg); max.d<- max(deg)
spa <- 10/(max.d - min.d) # how much to increment 0 to 10 space along y-axis
divi.y.1 <- seq(from = min.d, to=max.d, by = 1)
divi.y.2 <- seq(from = 0, to=10, by = spa) # both have same length
ind.x <- c(); ind.x[1] = 0
for(x in 2:n.nod){
ind.x[x] <- ind.x[x-1] + 0.1
if(ind.x[x] >= 10){
ind.x[x] = ind.x[x-1] - 0.1
}
}
d1 <- data.frame(divi.y.1, divi.y.2)
# plotting space of grid is (0,0), (0, 10), (10, 10), (10, 0)
for(i in 1:n.nod){
# y-axis in order
inD <- which(d1$divi.y.1 == deg[i])
mat.c[i, 2] <- d1[inD,2]
}
mat.c[, 1] <- ind.x
return(data.frame(mat.c))
}
这是绘制igraph
对象的“老式”方式:
# plot igraph object - the old fashion way
x11()
plot(g1, layout = coord(g1), rescale = T, frame=T,
vertex.frame.color = "black", edge.color = "lightsteelblue",
edge.width = 1, vertex.label.cex = 1,
vertex.label.color = "black",
main = "Nodes in order of degree: top have more links, bottom fewer links")
ggraph
文档的链接是here。另请参阅ggraph
的GitHub存储库以获取软件包安装说明(需要&gt; R.3.3版本)。下面是工作的ggraph图(但我没有指定每个节点的坐标):
library(ggraph)
V(g1)$NaMe <- seq(1:20)
x11()
ggraph(g1, 'igraph', algorithm = 'kk') +
geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) +
geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: How to allocate coordinate for each node?") +
ggforce::theme_no_axes()
这是我尝试使用每个节点的指定坐标制作ggraph
图。在ggraph()
中类似的示例和早期尝试将节点的坐标传递到绘图上之后,我尝试了以下操作:
g <- make_ring(10) + make_full_graph(5)
coords <- layout_(g, as_star())
plot(g, layout = coords)
# try to replicate this example:
coords2 <- add_layout_(g1, coord(g1))
还尝试使用this function。这很困难,因为文档中没有示例。
Lay <- layout_igraph_manual(g1, coord(g1))
Lay <- layout_igraph_igraph(g1, coord(g1))
x11()
ggraph(g1, 'igraph', algorithm = 'kk' ) + add_layout_(Lay) +
# layout_igraph_circlepack() +
geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) +
geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: Cannot allocate coordinate for each node") +
ggforce::theme_no_axes()
答案 0 :(得分:2)
我认为作者无意直接致电layout_igraph_manual
。如果将布局命名为“manual”,则可以传递手动布局顶点所需的参数。如果我理解正确的话,这就让我了解你的目标:
coords <- coord(g1)
names(coords) <- c("x","y")
coords <- as.data.frame(coords)
ggraph(g1, layout = "manual", circular = FALSE, node.positions = coords)+
geom_edge_link(colour = "black", alpha = 0.8, show.legend = F) +
geom_node_label(aes(label = NaMe)) + ggtitle("ggraph plot: How to allocate coordinate for each node?") +
ggforce::theme_no_axes()
根据文档,您的手动布局是一个数据框并且包含x
和y
列非常重要。我已经对coord()
函数的输出执行了此操作。您可能只想更新它以返回该表单中的数据。
答案 1 :(得分:1)
使用ggraph时,通常不必考虑节点坐标 - 它们是根据所选布局自动提供的。如果您想事先自己计算布局,只需使用手动布局 - 查看layout_igraph_manual
的文档
答案 2 :(得分:1)
谢谢@ThomasP85(哇!ggraph的开发人员)。在这个例子中,我想指定每个节点的坐标。我已经尝试了layout_igraph_manual
,layout_
,add_layout_
和其他许多人,似乎没有用。
这是什么工作
co2<- data.frame(coord(g1)) # my mistake above, the output of coord() should be a matrix
colnames(co2)<- c("x", "y")
Lay<- createLayout(g1, layout = "nicely") # try any layout
Lay$x<- co2$x # <== now overwrite their coordinates
Lay$y<- co2$y
x11() # <==== this is ggraph version of the igraph plot above
ggraph(graph=g1, data=Lay) +
geom_edge_link(colour = "black", alpha = 0.5, show.legend = F) +
geom_node_label(aes(label = NaMe)) + ggtitle("Nodes with higher degree at top, lower degree nodes at the bottom") +
ggforce::theme_no_axes()
@ ThomasP85如果您可以使用layout_igraph_manual
提供上述代码的工作示例,我们将不胜感激。