plotlabelsmap

This functions plots cell labels into a two-dimensional t-SNE map, UMAP, or a Fruchterman-Rheingold graph layout
of the singe-cell transcriptome data.

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

plotlabelsmap function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>labels</dt>
<dd>Vector of labels for all cells to be highlighted in the t-SNE map. The order has to be the same as for the
columns in slot <code>ndata</code> of the <code>SCseq</code> object. Default is <code>NULL</code> and cell names are highlighted.</dd>
<dt>fr</dt>
<dd>logical. If <code>TRUE</code> then plot Fruchterman-Rheingold layout. Default is <code>FALSE</code>.</dd>
<dt>um</dt>
<dd>logical. If <code>TRUE</code> then plot umap dimensional reduction representation. Default is <code>FALSE</code>.</dd>
<dt>cex</dt>
<dd>positive real number. Size of the labels. Default is 0.5.</dd></dl>

Arguments

Plot labels in a dimensional reduction representation — plotlabelsmap

<dl>

<dt>object</dt>
<dd><code>SCseq</code> class object.</dd>


<dt>labels</dt>
<dd>Vector of labels for all cells to be highlighted in the t-SNE map. The order has to be the same as for the
columns in slot <code>ndata</code> of the <code>SCseq</code> object. Default is <code>NULL</code> and cell names are highlighted.</dd>


<dt>fr</dt>
<dd>logical. If <code>TRUE</code> then plot Fruchterman-Rheingold layout. Default is <code>FALSE</code>.</dd>


<dt>um</dt>
<dd>logical. If <code>TRUE</code> then plot umap dimensional reduction representation. Default is <code>FALSE</code>.</dd>


<dt>cex</dt>
<dd>positive real number. Size of the labels. Default is 0.5.</dd>

</dl>

plotlabelsmap: Plot labels in a dimensional reduction representation

Description

Usage

Value

Arguments