plotNetwork: Plot differential network

In iDINGO: Integrative Differential Network Analysis in Genomics

Description

This function plots the differential network from a completed DINGO or iDINGO model.

Usage

plotNetwork(fit, threshold=0.05, thresh.type="p.val", layout="circular",
            legend.pos="left")

Arguments

fit	output from running dingo() or idingo()
threshold	a numeric value containing the threshold for which edges will be included in the differential network plot. If 'thresh.type' is 'p.val', all edges with p-values below this threshold will be included in the plot. If 'thresh.type' is 'diff.score', all edges with absolute differential scores above this threshold will be included in the plot.
thresh.type	either 'p.val' or 'diff.score', defining which variable is used as threshold for edge inclusion.
layout	either 'circular' or one of igraph's supported layouts. If 'circular', dingo networks will be plotted in a circle, and idingo networks will be plotted as a cylinder (with each platform/level as a separate circle).
legend.pos	Legend position for multi-platform networks, in c("left", "right"). Legend is not included for single-platform networks.

Value

visNet

a network plot, using igraph and visNetwork

Note

To calculate differential scores and p-values for use in network plot thresholding, diff.score must be set to TRUE in dingo() or idingo().

Author(s)

Caleb CLASS [e-mail], Min Jin HA [e-mail]

Examples

data(brca)

# Plot the iDINGO result using a p-value threshold of 0.01.
plotNetwork(brca$fit, threshold = 0.01, thresh.type = "p.val")

Example output

Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

iDINGO documentation built on July 30, 2020, 5:14 p.m.