R session aborts with "unrooted" layout option #383
Description
I started working on auto-generating a tree for an article figure, and got about this far before I had my R session abort every time I tried to plot this graph.
I had been using the "tree" layout, which worked fine except it added an extra root node when I already had included.
So I went to use the "unrooted" option and... well, every time I run that part of the code, my R session aborts and restarts.
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.1.1
tidyverse 2.0.0
ggraph 2.2.1
tidygraph 1.3.1
library(tidyverse)
library(ggraph)
library(tidygraph)
MNI = 4 # MNI - 1 = number of intersections
MAX_LEVEL = 2*(MNI - 1) + 3 # 2 levels per intersection (location inside/outside threshold and if intersection occurs) + initial node + starting location
node_tib <- tibble_row(
node_id = "0",
node_level = 1,
label = "root",
parent = NA,
has_children = TRUE,
value = NA) # init_node
level = 2
while(level < MAX_LEVEL){
for(parent_id in filter(node_tib, node_level == level - 1)$node_id){
if(filter(node_tib, node_id == parent_id)$has_children == TRUE){
if(level %% 2 == 1){ # odd number levels
# child 1
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"1"),
node_level = level,
label = "yes",
parent = parent_id,
has_children = TRUE,
value = NA)
# child 2
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"0"),
node_level = level,
label = "no",
parent = parent_id,
has_children = TRUE,
value = NA)
}
else if(level == 2){ # second level
# child 1
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"1"),
node_level = level,
label = "nucleus",
parent = parent_id,
has_children = TRUE,
value = NA)
# child 2
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"0"),
node_level = level,
label = "cytoplasm",
parent = parent_id,
has_children = TRUE,
value = NA)
}
else { # even number levels
# child 1
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"1"),
node_level = level,
label = "yes",
parent = parent_id,
has_children = TRUE,
value = NA)
# child 2
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"0"),
node_level = level,
label = "no",
parent = parent_id,
has_children = FALSE,
value = NA)
}
}
}
level <- level + 1
}
for(parent_id in filter(node_tib, node_level == level - 1)$node_id){
if(filter(node_tib, node_id == parent_id)$has_children == TRUE){
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"1"),
node_level = level,
label = "yes",
parent = parent_id,
has_children = FALSE,
value = NA)
node_tib <- add_row(node_tib,
node_id = paste0(parent_id,"0"),
node_level = level,
label = "no",
parent = parent_id,
has_children = FALSE,
value = NA)
}
}
graph <- as_tbl_graph(
data.frame(
from = node_tib$parent,
to = node_tib$node_id
)
)
graph
tree_plot <- ggraph(graph, layout="unrooted") +
geom_edge_link() +
geom_node_point(size=3, shape = 21, colour = "black", stroke = 1, fill = "white")
tree_plot