SpatialPlot

This function will plot information about beads and bins on x and y coordinates

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 

SpatialPlot function

<dl><dt>dat_long</dt>
<dd>data.table of bead expression intensities per gene with metadata in long format</dd>
<dt>vars</dt>
<dd>character vector of features to plot/columns of metadata</dd>
<dt>text_size</dt>
<dd>Ggplot2 text size</dd>
<dt>title_size</dt>
<dd>Ggplot2 title size</dd>
<dt>legend_size_pt</dt>
<dd>Ggplot2 legend_size_pt</dd>
<dt>legend_height_bar</dt>
<dd>Ggplot2 legend_height_bar</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Spatial plots of meta data — SpatialPlot

<dl>

<dt>dat_long</dt>
<dd>data.table of bead expression intensities per gene with metadata in long format</dd>


<dt>vars</dt>
<dd>character vector of features to plot/columns of metadata</dd>


<dt>text_size</dt>
<dd>Ggplot2 text size</dd>


<dt>title_size</dt>
<dd>Ggplot2 title size</dd>


<dt>legend_size_pt</dt>
<dd>Ggplot2 legend_size_pt</dd>


<dt>legend_height_bar</dt>
<dd>Ggplot2 legend_height_bar</dd>


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

</dl>

SpatialPlot: Spatial plots of meta data

Description

Usage

Value

Arguments