This function generates a co-occurrence network from a provided list and calculates strength and directionality of the relationships. The output can be passed to igraph to plot a directed acyclic graph (DAG).
Arguments
- mrBootstrap_obj
A list of bootstrapped partial dependencies output from
mrBootstrap().
Examples
library(tidymodels)
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library(igraph)
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library(ggnetwork)
mrIML_rf <- mrIML::mrIML_bird_parasites_RF
mrIML_rf_boot <- mrIML_rf %>%
mrBootstrap()
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assoc_net_filtered <- mrIML_rf_boot %>%
mrCoOccurNet() %>%
filter(mean_strength > 0.05)
# Convert to igraph
g <- graph_from_data_frame(
assoc_net_filtered,
directed = TRUE,
vertices = names(mrIML_rf$Data$Y)
)
E(g)$Value <- assoc_net_filtered$mean_strength
E(g)$Color <- ifelse(
assoc_net_filtered$direction == "negative",
"blue", "red"
)
# Convert the igraph object to a ggplot object with NMDS layout
gg <- ggnetwork(g)
# Plot the graph
ggplot(
gg,
aes(x = x, y = y, xend = xend, yend = yend)
) +
geom_edges(
aes(color = Color, linewidth = Value),
curvature = 0.2,
arrow = arrow(length = unit(5, "pt"), type = "closed")
) +
geom_nodes(
color = "gray",
size = degree(g, mode = "out") / 2
) +
scale_color_identity() +
theme_void() +
theme(legend.position = "none") +
geom_nodelabel_repel(
aes(label = name),
box.padding = unit(0.5, "lines"),
size = 2,
segment.colour = "black",
colour = "white",
fill = "grey36"
)
