get_num_clust

This function uses the Silhouette Method applied to CNV scores to determine the
best number of clusters to divide the binned beads into

This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").

Diane Zhang

SlideCNA

Calls Copy Number Alterations from Slide-Seq Data

Johanna Klughammer

Jan Watter

Broad Institute of MIT and Harvard 

get_num_clust function

<dl><dt>data</dt>
<dd>cnv_data list object of cnv data from SlideCNA::prep_cnv_dat()</dd>
<dt>hc_func</dt>
<dd>character string for which hierarchical clustering function to use</dd>
<dt>max_k</dt>
<dd>integer of number max number of clusters to evaluate (2:max_k)</dd>
<dt>plot</dt>
<dd>TRUE if plotting silhoutte scores per cluster</dd>
<dt>malig</dt>
<dd>TRUE if only using malignant bins and FALSE if using all bins</dd>
<dt>k</dt>
<dd>integer of optimal number of clusters, if known, and NA if not known</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Find optimal number of clusters — get_num_clust

<dl>

<dt>data</dt>
<dd>cnv_data list object of cnv data from SlideCNA::prep_cnv_dat()</dd>


<dt>hc_func</dt>
<dd>character string for which hierarchical clustering function to use</dd>


<dt>max_k</dt>
<dd>integer of number max number of clusters to evaluate (2:max_k)</dd>


<dt>plot</dt>
<dd>TRUE if plotting silhoutte scores per cluster</dd>


<dt>malig</dt>
<dd>TRUE if only using malignant bins and FALSE if using all bins</dd>


<dt>k</dt>
<dd>integer of optimal number of clusters, if known, and NA if not known</dd>


<dt>plot_directory</dt>
<dd>output plot directory path</dd>

</dl>

get_num_clust: Find optimal number of clusters

Description

Usage

Value

Arguments