plotNetwork function

Plot differential network

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

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.

Returns

• 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 caclass@mdanderson.org, Min Jin HA mjha@mdanderson.org

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")