plot_lucid: Visualize LUCID model through a Sankey diagram

In LUCIDus: LUCID with Multiple Omics Data

Visualize LUCID model through a Sankey diagram

Description

In the Sankey diagram, each node either represents a variable (exposure, omics or outcome) or a latent cluster. Each line represents an association. The color of the node represents variable type, either exposure, omics or outcome. The width of the line represents the effect size of a certain association; the color of the line represents the direction of a certain association. Only work for LUCID early for now.

Usage

plot_lucid(
  x,
  G_color = "dimgray",
  X_color = "#eb8c30",
  Z_color = "#2fa4da",
  Y_color = "#afa58e",
  pos_link_color = "#67928b",
  neg_link_color = "#d1e5eb",
  fontsize = 7
)

Arguments

x	A LUCID model fitted by estimate_lucid
G_color	Color of node for exposure
X_color	Color of node for latent cluster
Z_color	Color of node for omics data
Y_color	Color of node for outcome
pos_link_color	Color of link corresponds to positive association
neg_link_color	Color of link corresponds to negative association
fontsize	Font size for annotation

Value

A DAG graph created by sankeyNetwork

Examples

# prepare data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal
Y_binary <- sim_data$Y_binary
cov <- sim_data$Covariate

# plot lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
CoY = NULL, family = "normal", K = 2, seed = 1008)
plot_lucid(fit1)

# change node color
plot_lucid(fit1, G_color = "yellow")
plot_lucid(fit1, Z_color = "red")

# change link color
plot_lucid(fit1, pos_link_color = "red", neg_link_color = "green")

LUCIDus documentation built on Nov. 2, 2023, 5:21 p.m.