plot_networks: Plot a network (estimated from 'mdine') for each group

In kevinmcgregor/mdine: Microbiome Differential Network Estimation

Description

Plot a network (estimated from mdine) for each group

Usage

plot_networks(
  obj,
  v.col = NULL,
  e.col = NULL,
  lay0 = layout_in_circle,
  lay1 = layout_in_circle,
  lab0 = "Group 0",
  lab1 = "Group 1",
  scale_line_width = 30,
  vertex.size = 50,
  vertex.labs = NULL,
  vertex.label.cex = NULL
)

Arguments

obj	An object of class mdine
v.col	Vertex colours. If null, a colour blind-friendly pallete is used
e.col	Edge colour.
lay0	igraph layout for group 0
lay1	igraph layout for group 1
lab0	Main label for group 0 network
lab1	Main label for group 1 network
scale_line_width	Scaling factor for with of network edges
vertex.size	Scaling factor for vertex size
vertex.labs	Character vector containing vertex labels
vertex.label.cex	Scaling factor for vertex labels

Details

Plots an igraph-based network for each group. Note that this function has limited functionality and is intended only for immediate visualization of the networks. To plot more sophisticated networks, please use the adj2ig() function along with plot.igraph().

Examples

library(mdine)
data(crohns)

X <- model.matrix(~disease, data=crohns$covars)
md.fit <- mdine(Y=crohns$otu.counts, X=X, Z=X[,2], mc.cores=1, iter=1000)
plot_networks(md.fit)

kevinmcgregor/mdine documentation built on April 10, 2021, 4:18 a.m.