swaglm (version 0.0.1)

plot.swaglm_network: plot.swaglm_network

Description

Visualizes a SWAG network with discretized vertex size, optional edge width scaling, and edge coloring based on a correlation matrix.

Usage

# S3 method for swaglm_network
plot(x, bins = 5, scale_edge = NULL, size_range = c(8, 30), ...)

Value

None.

Arguments

x

An object of class swaglm_network

bins

Number of bins for vertex size discretization (default = 5)

scale_edge

Logical; whether to scale the edge width

size_range

A numeric vector of length 2 specifying the range of node sizes.

...

Additional arguments passed to igraph::plot

Examples

set.seed(12345)
n <- 2000
p <- 100

# create design matrix and vector of coefficients
Sigma <- diag(rep(1/p, p))
X <- MASS::mvrnorm(n = n, mu = rep(0, p), Sigma = Sigma)
beta = c(-15,-10,5,10,15, rep(0,p-5))

# --------------------- generate from logistic regression with an intercept of one
z <- 1 + X%*%beta
pr <- 1/(1 + exp(-z))
y <- as.factor(rbinom(n, 1, pr))
y = as.numeric(y)-1

# define swag parameters
quantile_alpha = .15
p_max = 20
swag_obj = swaglm::swaglm(X=X, y = y, p_max = p_max, family = stats::binomial(), 
                          alpha = quantile_alpha, verbose = TRUE, seed = 123)
names(swag_obj)
swag_network = swaglm::compute_network(swag_obj)
names(swag_network)
plot(swag_network)