greedyModularityCut

Performs a greedy top-down selective cut to optmize modularity

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

greedyModularityCut function

<dl><dt>wt</dt>
<dd>walktrap result</dd>
<dt>N</dt>
<dd>numeric Number of top greedy splits to take</dd>
<dt>leaf.labels</dt>
<dd>leaf sample label factor, for breadth calculations - must be a named factor containing all wt$names, or if wt$names is null, a factor listing cells in the same order as wt leafs (default=NULL)</dd>
<dt>minsize</dt>
<dd>numeric Minimum size of the branch (in number of leafs) (default=0)</dd>
<dt>minbreadth</dt>
<dd>numeric Minimum allowed breadth of a branch (measured as normalized entropy) (default=0)</dd>
<dt>flat.cut</dt>
<dd>boolean Whether to simply take a flat cut (i.e. follow provided tree; default=TRUE). Does no observe minsize/minbreadth restrictions</dd></dl>

Arguments

Performs a greedy top-down selective cut to optmize modularity — greedyModularityCut

<dl>

<dt>wt</dt>
<dd>walktrap result</dd>


<dt>N</dt>
<dd>numeric Number of top greedy splits to take</dd>


<dt>leaf.labels</dt>
<dd>leaf sample label factor, for breadth calculations - must be a named factor containing all wt$names, or if wt$names is null, a factor listing cells in the same order as wt leafs (default=NULL)</dd>


<dt>minsize</dt>
<dd>numeric Minimum size of the branch (in number of leafs) (default=0)</dd>


<dt>minbreadth</dt>
<dd>numeric Minimum allowed breadth of a branch (measured as normalized entropy) (default=0)</dd>


<dt>flat.cut</dt>
<dd>boolean Whether to simply take a flat cut (i.e. follow provided tree; default=TRUE). Does no observe minsize/minbreadth restrictions</dd>

</dl>

greedyModularityCut: Performs a greedy top-down selective cut to optmize modularity

Description

Usage

Value

Arguments