plotComponentVariance

Requires buildGraph() or updatePairs() to be ran first with the argument score.component.variance=TRUE.

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Evan Biederstedt

conos

Clustering on Network of Samples

Viktor Petukhov

Nikolas Barkas

Peter Kharchenko

Weiliang Qiu

plotComponentVariance function

<dl><dt>conos.obj</dt>
<dd>conos object</dd>
<dt>space</dt>
<dd>character Reduction space to be analyzed (currently, component variance scoring is only supported by PCA and CPCA) (default='PCA')</dd>
<dt>plot.theme</dt>
<dd>ggplot theme (default=ggplot2::theme_bw()). Refer to &lt;https://ggplot2.tidyverse.org/reference/ggtheme.html&gt; for more details.</dd></dl>

Arguments

Plot fraction of variance explained by the successive reduced space components (PCA, CPCA) — plotComponentVariance

<dl>

<dt>conos.obj</dt>
<dd>conos object</dd>


<dt>space</dt>
<dd>character Reduction space to be analyzed (currently, component variance scoring is only supported by PCA and CPCA) (default='PCA')</dd>


<dt>plot.theme</dt>
<dd>ggplot theme (default=ggplot2::theme_bw()). Refer to &lt;https://ggplot2.tidyverse.org/reference/ggtheme.html&gt; for more details.</dd>

</dl>

plotComponentVariance: Plot fraction of variance explained by the successive reduced space components (PCA, CPCA)

Description

Usage

Value

Arguments