equSA (version 1.1.5)

plotJGraph: Plot Networks

Description

Plot multiple networks with specific layout.

Usage

plotJGraph(A,fn="Net",th = 1e-06, mylayout = NULL)

Arguments

A

An array of multiple adjacency matrices of networks to be plotted which is a Mxpxp array. M is the number of dataset groups, p is the dimension of variables in each group.

fn

file name to save the network plots. Default to be an string called "Net". NOTE: It should be file name for PDF file.

th

numeric value, default to 1e-06. To specify the threshold if the estimated coefficient between two variables is to be considered connected.

mylayout

graph layout to draw networks, default to NULL.

Value

Returns the multiple layout objects from igraph package - numeric matrix of two columns and the rows with the same number as the number of vertices.

Details

This function serves as the alternative plotting function to allow users to plot multiple networks with specific layout, such as plotting the simulated networks.

References

Allen, G.I., and Liu, Z. (2012). A Log-Linear graphical model for inferring genetic networks from high-throughput sequencing data. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012).

Jia, B. and Liang, F. (2017) Joint Estimation of Multiple Gaussian Graphical Models via Multiple Hypothesis Tests (preparing)

Examples

# NOT RUN {
#library(equSA)
#data(SR0)
#data(TR0)
#data_all <- vector("list",2)
#data_all[[1]] <- SR0
#data_all[[2]] <- TR0
#A <- JGGM(data_all,ALPHA1=0.05,ALPHA2=0.01)$Array
#plotJGraph(A)
# }