cape (version 2.0.2)

plotPhenoCor: Plot correlations between phenotype pairs.

Description

This function plots pairs of phenotypes against each other to examine phenotype correlations. CAPE performs best when phenotypes are moderately correlated (0.4 < r < 0.8). This script can help prioritize phenotypes for use in CAPE. Phenotype pairs are plotted in a panel in which the lower triangle shows points colored by the indicated covariate, and the upper triangle shows correlation statistics.

Usage

plotPhenoCor(data.obj, pheno.which = NULL, 
color.by = NULL, group.labels = NULL, 
text.cex = 1, pheno.labels = NULL)

Arguments

data.obj

The object in which all results are stored. See read.population.

pheno.which

A vector of character strings indicating which phenotypes should be plotted. If pheno.which is NULL, all phenotypes will be plotted.

color.by

A vector of character strings indicating how the points should be colored. Points are colored based on covariates. These covariates must be specified using pheno2covar or marker2covar before they can be recognized by this function.

group.labels

A vector of character strings naming the groups that are specified by the covariates. For example, if coloring by the covariate "sex," coded as 0 for females and 1 for males, the group labels would be c("female", "male"). The vector must be the same length as the number of groups, and must match the numerical order of the groups.

text.cex

A numerical value indicating the size of the text showing the correlation values between phenotypes.

pheno.labels

An optional vector of character strings giving alternate names for the phenotypes being plotted.

See Also

pheno2covar, marker2covar, plotPheno