.plotXVsY.bexy

Function to plot X vs Y counts and color them according to BeXY posterior mode

internal

Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (<https://bitbucket.org/wegmannlab/bexy>), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.

Madleina Caduff

bexy

Visualize and Parse the Output of 'BeXY'

Raphael Eckel

Christoph Leuenberger

Daniel Wegmann

.plotXVsY.bexy function

<dl><dt>object</dt>
<dd>A bexy object.</dd>
<dt>ix_X</dt>
<dd>An integer representing the index of the scaffold to be plotted on the x-axis.</dd>
<dt>ix_Y</dt>
<dd>An integer representing the index of the scaffold to be plotted on the y-axis.</dd>
<dt>colors</dt>
<dd>A vector of length three with the colors for aneuploid, XX and XY samples, respectively.</dd>
<dt>sampleNamesToHighlight</dt>
<dd>A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities.</dd>
<dt>label</dt>
<dd>Boolean indicating whether samples should be labeled.</dd>
<dt>...</dt>
<dd>Other parameters used for plotting</dd></dl>

Arguments

Function to plot X vs Y counts and color them according to BeXY posterior mode — .plotXVsY.bexy

<dl>

<dt>object</dt>
<dd>A bexy object.</dd>


<dt>ix_X</dt>
<dd>An integer representing the index of the scaffold to be plotted on the x-axis.</dd>


<dt>ix_Y</dt>
<dd>An integer representing the index of the scaffold to be plotted on the y-axis.</dd>


<dt>colors</dt>
<dd>A vector of length three with the colors for aneuploid, XX and XY samples, respectively.</dd>


<dt>sampleNamesToHighlight</dt>
<dd>A vector of sample names that should be highlighted. If empty, samples are automatically highlighted based on the posterior probabilities.</dd>


<dt>label</dt>
<dd>Boolean indicating whether samples should be labeled.</dd>


<dt>...</dt>
<dd>Other parameters used for plotting</dd>

</dl>

.plotXVsY.bexy: Function to plot X vs Y counts and color them according to BeXY posterior mode

Description

Usage

Value

Arguments