cnv_heatmap

This function prepares data for plotting and makes a heat map of CNV scores per bead across all genes

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 

cnv_heatmap function

<dl><dt>cnv_data</dt>
<dd>list object of cnv data from SlideCNA::prep_cnv_dat()</dd>
<dt>md</dt>
<dd>data.table of metadata of each bead</dd>
<dt>chrom_colors</dt>
<dd>vector of colors labeled by which chromosome they correspond to</dd>
<dt>hc_function</dt>
<dd>character for which hierarchical clustering function to use</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Plot CNV scores on a heat map — cnv_heatmap

<dl>

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


<dt>md</dt>
<dd>data.table of metadata of each bead</dd>


<dt>chrom_colors</dt>
<dd>vector of colors labeled by which chromosome they correspond to</dd>


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


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

</dl>

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cnv_heatmap: Plot CNV scores on a heat map

Description

Usage

Value

Arguments