plot.mappoly.homoprob

Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologous chromosomes. For situations where pairwise
analysis has limited power, the algorithm relies on the multilocus
likelihood obtained through a hidden Markov model (HMM).
For more detail, please see Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.

Marcelo Mollinari

mappoly

Genetic Linkage Maps in Autopolyploids

Gabriel Gesteira

Cristiane Taniguti

Jeekin Lau

Oscar Riera-Lizarazu

Guilhereme Pereira

Augusto Garcia

Zhao-Bang Zeng

Katharine Preedy

Robert Gentleman

Ross Ihaka

R Foundation 

R-core 

plot.mappoly.homoprob function

<dl><dt>x</dt>
<dd>an object of class <code>mappoly.homoprob</code></dd>
<dt>stack</dt>
<dd>logical. If <code>TRUE</code>, probability profiles of all homologues
are stacked in the plot (default = FALSE)</dd>
<dt>lg</dt>
<dd>indicates which linkage group should be plotted. If <code>NULL</code> 
(default), it plots the first linkage group. If 
<code>"all"</code>, it plots all linkage groups</dd>
<dt>ind</dt>
<dd>indicates which individuals should be plotted. It can be the 
position of the individuals in the dataset or it's name. 
If <code>NULL</code> (default), the function plots the first 
individual</dd>
<dt>use.plotly</dt>
<dd>if <code>TRUE</code> (default), it uses plotly interactive graphic</dd>
<dt>verbose</dt>
<dd>if <code>TRUE</code> (default), the current progress is shown; if
<code>FALSE</code>, no output is produced</dd>
<dt>...</dt>
<dd>unused arguments</dd></dl>

Arguments

Plots mappoly.homoprob — plot.mappoly.homoprob

<dl>

<dt>x</dt>
<dd>an object of class <code>mappoly.homoprob</code></dd>


<dt>stack</dt>
<dd>logical. If <code>TRUE</code>, probability profiles of all homologues
are stacked in the plot (default = FALSE)</dd>


<dt>lg</dt>
<dd>indicates which linkage group should be plotted. If <code>NULL</code> 
(default), it plots the first linkage group. If 
<code>"all"</code>, it plots all linkage groups</dd>


<dt>ind</dt>
<dd>indicates which individuals should be plotted. It can be the 
position of the individuals in the dataset or it's name. 
If <code>NULL</code> (default), the function plots the first 
individual</dd>


<dt>use.plotly</dt>
<dd>if <code>TRUE</code> (default), it uses plotly interactive graphic</dd>


<dt>verbose</dt>
<dd>if <code>TRUE</code> (default), the current progress is shown; if
<code>FALSE</code>, no output is produced</dd>


<dt>...</dt>
<dd>unused arguments</dd>

</dl>

Plots mappoly.homoprob

plot.mappoly.homoprob: Plots mappoly.homoprob

Description

Usage

Arguments