plot_bars

This internal function is called by 
<code>plot_effects</code> to generate a 
bar plot showing mean trait values for all
combinations of genotypes for two markers.
This function also indicates the predicted
additive effects of the two markers with 
a dashed line, as well as the error of the
predicted additive effect with an orange box.
The true effect of the marker combination is
shown with a gray bar. 
The effects can centered on the reference
allele to better show relative effects of 
each allele and allele combination.

internal

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_bars function

<dl><dt>phenoV</dt>
<dd>A vector of trait values</dd>
<dt>marker1_vals</dt>
<dd>A vector of genotype values 
for marker1</dd>
<dt>marker2_vals</dt>
<dd>A vector of genotype values
for marker2.</dd>
<dt>pheno_name</dt>
<dd>A string indicating the name of
the trait being plotted.</dd>
<dt>marker1_label</dt>
<dd>A string indicating the name
of marker1</dd>
<dt>marker2_label</dt>
<dd>A string indicating the name
of marker2</dd>
<dt>ymin</dt>
<dd>A numeric value indicating the minimum 
y value for the plot. If NULL, it will be calculated
based on phenoV and error bars.</dd>
<dt>ymax</dt>
<dd>A numeric value indicating the maximum
y value for the plot. If NULL, it will be calculated
based on phenoV and error bars.</dd>
<dt>error_bars</dt>
<dd>A string indicating the type of error
bars to draw. Can be "sd" for standard deviation, "se"
for standard error, or "none".</dd>
<dt>ref_centered</dt>
<dd>Whether to center the effects
on the reference genotype.</dd></dl>

Arguments

Plot phenotypic effect for two markers as a bar plot — plot_bars

<dl>

<dt>phenoV</dt>
<dd>A vector of trait values</dd>


<dt>marker1_vals</dt>
<dd>A vector of genotype values 
for marker1</dd>


<dt>marker2_vals</dt>
<dd>A vector of genotype values
for marker2.</dd>


<dt>pheno_name</dt>
<dd>A string indicating the name of
the trait being plotted.</dd>


<dt>marker1_label</dt>
<dd>A string indicating the name
of marker1</dd>


<dt>marker2_label</dt>
<dd>A string indicating the name
of marker2</dd>


<dt>ymin</dt>
<dd>A numeric value indicating the minimum 
y value for the plot. If NULL, it will be calculated
based on phenoV and error bars.</dd>


<dt>ymax</dt>
<dd>A numeric value indicating the maximum
y value for the plot. If NULL, it will be calculated
based on phenoV and error bars.</dd>


<dt>error_bars</dt>
<dd>A string indicating the type of error
bars to draw. Can be "sd" for standard deviation, "se"
for standard error, or "none".</dd>


<dt>ref_centered</dt>
<dd>Whether to center the effects
on the reference genotype.</dd>

</dl>

Plot phenotypic effect for two markers as a bar plot

plot_bars: Plot phenotypic effect for two markers as a bar plot

Description

Usage

Value

Arguments