plotClusterBarplots

Plots barplots per sample of composition of each pagoda2 application based on
selected clustering

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

plotClusterBarplots function

<dl><dt>conos.obj</dt>
<dd>A conos object (default=NULL)</dd>
<dt>clustering</dt>
<dd>name of clustering in the current object (default=NULL)</dd>
<dt>groups</dt>
<dd>arbitrary grouping of cells (to use instead of the clustering) (default=NULL)</dd>
<dt>sample.factor</dt>
<dd>a factor describing cell membership in the samples (or some other category) (default=NULL). This will default to samples if not provided.</dd>
<dt>show.entropy</dt>
<dd>boolean Whether to include entropy barplot (default=TRUE)</dd>
<dt>show.size</dt>
<dd>boolean Whether to include size barplot (default=TRUE)</dd>
<dt>show.composition</dt>
<dd>boolean Whether to include composition barplot (default=TRUE)</dd>
<dt>legend.height</dt>
<dd>numeric Relative hight of the legend panel (default=0.2)</dd></dl>

Arguments

Plots barplots per sample of composition of each pagoda2 application based on
selected clustering — plotClusterBarplots

<dl>

<dt>conos.obj</dt>
<dd>A conos object (default=NULL)</dd>


<dt>clustering</dt>
<dd>name of clustering in the current object (default=NULL)</dd>


<dt>groups</dt>
<dd>arbitrary grouping of cells (to use instead of the clustering) (default=NULL)</dd>


<dt>sample.factor</dt>
<dd>a factor describing cell membership in the samples (or some other category) (default=NULL). This will default to samples if not provided.</dd>


<dt>show.entropy</dt>
<dd>boolean Whether to include entropy barplot (default=TRUE)</dd>


<dt>show.size</dt>
<dd>boolean Whether to include size barplot (default=TRUE)</dd>


<dt>show.composition</dt>
<dd>boolean Whether to include composition barplot (default=TRUE)</dd>


<dt>legend.height</dt>
<dd>numeric Relative hight of the legend panel (default=0.2)</dd>

</dl>

plotClusterBarplots: Plots barplots per sample of composition of each pagoda2 application based on selected clustering

Description

Usage

Value

Arguments