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cape (version 2.0.2)

plotNetwork: Plot the final epistatic network

Description

This function plots the final results with a using a different layout than plotVariantInfluences. Instead of the adjacency matrix, this function plots interactions between markers with arrows indicating the direction of influence. The function get.network must be run before plotting the network.

Usage

plotNetwork(data.obj, collapsed.net = TRUE, 
trait = NULL, phenotype.labels = NULL, 
main.lwd = 4, inter.lwd = 3, label.cex = 1.5, 
percent.bend = 15, chr.gap = 1, label.gap = 5, 
positive.col = "brown", negative.col = "blue")

Arguments

data.obj
The object in which all results are stored. See read.population.
collapsed.net
A logical value. If TRUE, a network condensed by linkage (see get.network) is plotted. If FALSE, the full network is plotted.
trait
A character vector indicating which traits should be plotted. If NULL, all traits are plotted.
phenotype.labels
A vector of strings listing alternate names for the phenotypes.
main.lwd
A numeric value specifying the line width of the main effects bars surrounding the chromosome bars.
inter.lwd
A numeric value specifying the line width of the interaction arrows drawn inside the chromosome circle
label.cex
A numberic value specifying the size of the chromomsome labels.
percent.bend
A numeric value between 0 and 100 specifying how much curvature should be added to the arrows within the circle.
chr.gap
A numeric value between 0 and 100 indicating what percentage of the circle should be devoted to individual gaps between chromosomes.
label.gap
A numeric value between 0 and 100 indicating what percentage of the circle should be devoted to the phenotype labels.
positive.col
The color in which to plot the postive values. Colors can be one of the following: "green", "purple", "orange", "blue", "brown", "yellow", or "gray."

negative.col
The color in which to plot the negative values. Colors can be one of the following: "green", "purple", "orange", "blue", "brown", "yellow", or "gray."

See Also

get.network, plotVariantInfluences

Examples

Run this code
## Not run: 
# 	plotNetwork(obesity.cross, collapsed.net = TRUE)
# 	plotNetwork(obesity.cross, collapsed.net = FALSE)
# 	plotNetwork(obesity.cross, collapsed.net = TRUE, trait = "glucose")
# 	## End(Not run)

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