cape (version 2.0.2)

plotPheno: Plot phenotype values by individual.

Description

This function plots phenotype values by individual, and can color points based on covariates if desired.

Usage

plotPheno(data.obj, pheno.which = NULL, 
color.by = NULL, group.labels = NULL, 
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.

pheno.labels

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

See Also

pheno2covar, marker2covar, plotPhenoCor