plotSVD


	The object in which all results are stored. See <code><a rd-options="" href="/link/read.population?package=cape&version=2.0.2" data-mini-rdoc="cape::read.population">read.population</a></code>.


data.obj


	A character string ("vertical", or "horizontal") indicating whether the plot should be vertically or horizontally oriented.


orientation


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

neg.col


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

pos.col


	 	Either "light" or "dark" depending on the desired range of colors used.
	 

light.dark


This function plots the results of the singular value decomposition (SVD) of the phenotype matrix. This plot is useful for selecting eigentraits for further analysis.


hplot

Combines complementary information across multiple related
phenotypes to infer directed epistatic interactions between genetic markers.
This analysis can be applied to a variety of engineered and natural populations.

Anna L Tyler

cape

Combined Analysis of Pleiotropy and Epistasis

plotSVD function


	The object in which all results are stored. See <code><a rd-options='' href='read.population'>read.population</a></code>.


plotSVD: Plot the results of the singular value decomposition of the phenotype matrix

Description

Usage

Arguments

Value

See Also