plot_pheno_cor

a <code><a rd-options="" href="/link/Cape?package=cape&version=3.1.1" data-mini-rdoc="cape::Cape">Cape</a></code> object

data_obj

A vector of trait names to plot. The default is to plot all traits.

pheno_which

A character string indicating a value to color the traits by, for example sex or treatment.
It must be one of the covariates. See <code><a rd-options="" href="/link/pheno2covar?package=cape&version=3.1.1" data-mini-rdoc="cape::pheno2covar">pheno2covar</a></code>.

color_by

A vector of names for the legend indicating the groups for the colored dots.

group_labels

A numeric value indicating the size of the text

text_cex

A vector of names for traits to appear in the plot in case the column names are not very pretty.

pheno_labels

A numeric value indicating the size of the points.

pt_cex

This function plots pairs of traits against each other
to visualize the correlations between traits.

Combined Analysis of Pleiotropy and Epistasis infers predictive
networks between genetic variants and phenotypes. It can be used with
standard two-parent populations as well as multi-parent populations, such
as the Diversity Outbred (DO) mice, Collaborative Cross (CC) mice, or the
multi-parent advanced generation intercross (MAGIC) population of Arabidopsis
thaliana. It uses complementary information of pleiotropic gene variants across
different phenotypes to resolve models of epistatic interactions between alleles.
To do this, cape reparametrizes main effect and interaction coefficients from
pairwise variant regressions into directed influence parameters. These
parameters describe how alleles influence each other, in terms of suppression
and enhancement, as well as how gene variants influence phenotypes. All of the
final interactions are reported as directed interactions between pairs of
parental alleles. For detailed descriptions of the methods used in this package
please see the following references.
Carter, G. W., Hays, M., Sherman, A. & Galitski, T. (2012) <doi:10.1371/journal.pgen.1003010>.
Tyler, A. L., Lu, W., Hendrick, J. J., Philip, V. M. & Carter, G. W. (2013) <doi:10.1371/journal.pcbi.1003270>.

Anna L Tyler

cape

Combined Analysis of Pleiotropy and Epistasis for Diversity
Outbred Mice

Anna Tyler

Jake Emerson

Baha El Kassaby

Ann Wells

Georgi Kolishovski

Vivek Philip

Gregory Carter

plot_pheno_cor function

<dl><dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>
<dt>pheno_which</dt>
<dd>A vector of trait names to plot. The default is to plot all traits.</dd>
<dt>color_by</dt>
<dd>A character string indicating a value to color the traits by, for example sex or treatment.
It must be one of the covariates. See <code>pheno2covar</code>.</dd>
<dt>group_labels</dt>
<dd>A vector of names for the legend indicating the groups for the colored dots.</dd>
<dt>text_cex</dt>
<dd>A numeric value indicating the size of the text</dd>
<dt>pheno_labels</dt>
<dd>A vector of names for traits to appear in the plot in case the column names are not very pretty.</dd>
<dt>pt_cex</dt>
<dd>A numeric value indicating the size of the points.</dd></dl>

Arguments

Plot trait pairs against each other — plot_pheno_cor

<dl>

<dt>data_obj</dt>
<dd>a <code>Cape</code> object</dd>


<dt>pheno_which</dt>
<dd>A vector of trait names to plot. The default is to plot all traits.</dd>


<dt>color_by</dt>
<dd>A character string indicating a value to color the traits by, for example sex or treatment.
It must be one of the covariates. See <code>pheno2covar</code>.</dd>


<dt>group_labels</dt>
<dd>A vector of names for the legend indicating the groups for the colored dots.</dd>


<dt>text_cex</dt>
<dd>A numeric value indicating the size of the text</dd>


<dt>pheno_labels</dt>
<dd>A vector of names for traits to appear in the plot in case the column names are not very pretty.</dd>


<dt>pt_cex</dt>
<dd>A numeric value indicating the size of the points.</dd>

</dl>

plot_pheno_cor: Plot trait pairs against each other

Description

Usage

Arguments

Examples