iDINGO (version 1.0.4)

plotNetwork: Plot differential network

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

Examples

# NOT RUN {
data(brca)

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