plotVarFeatures

For each dataset where the feature variablitity is calculated,
a plot of log10 feature expression variance and log10 mean will be produced.
Features that are considered as variable would be highlighted in red.

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

Andrew Robbins

plotVarFeatures function

<dl><dt>object</dt>
<dd>liger object. <code>selectGenes</code> needs to
be run in advance.</dd>
<dt>combinePlot</dt>
<dd>Logical. If <code>TRUE</code>, sub-figures for all datasets will
be combined into one plot. if <code>FALSE</code>, a list of plots will be returned.
Default <code>TRUE</code>.</dd>
<dt>dotSize</dt>
<dd>Controls the size of dots in the main plot. Default
<code>0.8</code>.</dd>
<dt>...</dt>
<dd>More theme setting parameters passed to
<code>.ggplotLigerTheme</code>.</dd></dl>

Arguments

Plot the variance vs mean of feature expression — plotVarFeatures

<dl>

<dt>object</dt>
<dd>liger object. <code>selectGenes</code> needs to
be run in advance.</dd>


<dt>combinePlot</dt>
<dd>Logical. If <code>TRUE</code>, sub-figures for all datasets will
be combined into one plot. if <code>FALSE</code>, a list of plots will be returned.
Default <code>TRUE</code>.</dd>


<dt>dotSize</dt>
<dd>Controls the size of dots in the main plot. Default
<code>0.8</code>.</dd>


<dt>...</dt>
<dd>More theme setting parameters passed to
<code>.ggplotLigerTheme</code>.</dd>

</dl>

Plot the variance vs mean of feature expression

plotVarFeatures: Plot the variance vs mean of feature expression

Description

Usage

Value

Arguments

Examples