PlotSickleJrUMAP

Plot the first and second dimensions of a UMAP dimension reduction
and color either by clustering results or metadata.

Methods to perform Joint graph Regularized Single-Cell Kullback-Leibler Sparse Non-negative Matrix Factorization ('jrSiCKLSNMF', pronounced "junior sickles NMF") on quality controlled single-cell multimodal omics count data. 'jrSiCKLSNMF' specifically deals with dual-assay scRNA-seq and scATAC-seq data. This package contains functions to extract meaningful latent factors that are shared across omics modalities. These factors enable accurate cell-type clustering and facilitate visualizations. Methods for pre-processing, clustering, and mini-batch updates and other adaptations for larger datasets are also included. For further details on the methods used in this package please see Ellis, Roy, and Datta (2023) <doi:10.3389/fgene.2023.1179439>.

Dorothy Ellis

jrSiCKLSNMF

Multimodal Single-Cell Omics Dimensionality Reduction

Susmita Datta

Kenneth Perkins

Renaud Gaujoux

PlotSickleJrUMAP function

<dl><dt>SickleJr</dt>
<dd>An object of class SickleJr</dd>
<dt>umap.modality</dt>
<dd>String corresponding to the name of the UMAP of interest: defaults to <code>"H"</code></dd>
<dt>cluster</dt>
<dd>String input that indicates which cluster to color by: defaults to <code>"kmeans"</code></dd>
<dt>title</dt>
<dd>String input for optional <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></code> plot title</dd>
<dt>colorbymetadata</dt>
<dd>Name of metadata column if coloring by metadata</dd>
<dt>legendname</dt>
<dd>String input that to allow specification of a different legend name</dd></dl>

Arguments

Generate UMAP plots for an object of class SickleJr — PlotSickleJrUMAP

<dl>

<dt>SickleJr</dt>
<dd>An object of class SickleJr</dd>


<dt>umap.modality</dt>
<dd>String corresponding to the name of the UMAP of interest: defaults to <code>"H"</code></dd>


<dt>cluster</dt>
<dd>String input that indicates which cluster to color by: defaults to <code>"kmeans"</code></dd>


<dt>title</dt>
<dd>String input for optional <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> plot title</dd>


<dt>colorbymetadata</dt>
<dd>Name of metadata column if coloring by metadata</dd>


<dt>legendname</dt>
<dd>String input that to allow specification of a different legend name</dd>

</dl>

PlotSickleJrUMAP: Generate UMAP plots for an object of class SickleJr

Description

Usage

Value

Arguments

References

Examples