quantile_plot

This function colors and plots each bin by its CNV score quantiles (min, 1st quartile, median, 3rd quartile, max)
on spatial coordinates for each chromosome

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 

quantile_plot function

<dl><dt>cnv_data</dt>
<dd>list object of cnv data from SlideCNA::prep_cnv_dat()</dd>
<dt>cluster_label</dt>
<dd>character string of which column name to keep</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>legend_height_bar</dt>
<dd>integer of bar height of legend for ggplot</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Plot CNV score quantiles per bin and per chromosome — quantile_plot

<dl>

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


<dt>cluster_label</dt>
<dd>character string of which column name to keep</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>legend_height_bar</dt>
<dd>integer of bar height of legend for ggplot</dd>


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

</dl>

quantile_plot: Plot CNV score quantiles per bin and per chromosome

Description

Usage

Value

Arguments