find_go_terms

This function utilizes cluster-specific DEGs to identify cluster-specifc GO biological processes
and plots these if they occur

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 

find_go_terms function

<dl><dt>cluster_markers_obj</dt>
<dd>list object with cluster marker information</dd>
<dt>type</dt>
<dd>character string that is 'all' if using malignant and normal clusters and 'malig'
if just using malignant clusters</dd>
<dt>n_terms</dt>
<dd>integer of number of top DEGs to plot/use</dd>
<dt>text_size</dt>
<dd>integer of text size for ggplot</dd>
<dt>title_size</dt>
<dd>integer of title size for ggplot</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Find and plot top n GO-enriched terms per cluster — find_go_terms

<dl>

<dt>cluster_markers_obj</dt>
<dd>list object with cluster marker information</dd>


<dt>type</dt>
<dd>character string that is 'all' if using malignant and normal clusters and 'malig'
if just using malignant clusters</dd>


<dt>n_terms</dt>
<dd>integer of number of top DEGs to plot/use</dd>


<dt>text_size</dt>
<dd>integer of text size for ggplot</dd>


<dt>title_size</dt>
<dd>integer of title size for ggplot</dd>


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

</dl>

find_go_terms: Find and plot top n GO-enriched terms per cluster

Description

Usage

Value

Arguments