network {easybgm} | R Documentation |
Network plot
Description
The network plot visualizes the strength of interactions between two nodes, the partial associations. Solely edges with a posterior inclusion probability larger than the exc_prob
argument (default = 0.5) are shown. Edge thickness and saturation represent the strength of the association; the thicker the edge, the stronger the association. Red edges indicate negative relations and blue edges indicate positive associations.
Usage
plot_network(output, exc_prob = 0.5, evidence_thresh = 10, dashed = FALSE, ...)
Arguments
output |
Output object from the easybgm function. Supports also objects from the bgm function of the |
exc_prob |
The threshold for excluding edges. All edges with a lower inclusion probability will not be shown. The default is set to 0.5 in line with the median probability plot. |
evidence_thresh |
If dashed = TRUE, users can specify the threshold for sufficient evidence for inclusion. All edges with evidence lower than |
dashed |
A binary parameter indicating whether edges with inconclusive evidence should be dashed. Default is FALSE |
... |
Additional arguments passed onto |
Value
Returns a plot
Examples
library(easybgm)
library(bgms)
data <- na.omit(Wenchuan)
fit <- easybgm(data, type = "continuous",
iter = 1000 # for demonstration only (> 5e4 recommended)
)
plot_network(fit)
# Shows all edges with an inclusion probability larger than 0.1
plot_network(fit, exc_prob = 0.1)
# Indicate which edges have insufficient evidence for inclusion through a dashed line
plot_network(fit, dashed = TRUE, evidence_thresh = 10)