plotmap

This functions plots 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

plotmap function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>final</dt>
<dd>logical. If <code>TRUE</code>, then highlight final clusters after outlier identification. If <code>FALSE</code>, then highlight initial
clusters prior to outlier identification. Default is <code>TRUE</code>.</dd>
<dt>tp</dt>
<dd>Number between 0 and 1 to change transparency of dots in the map. Default is 1.</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>size of data points. Default value is 0.5.</dd></dl>

Arguments

Plotting a dimensional reduction representation — plotmap

<dl>

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


<dt>final</dt>
<dd>logical. If <code>TRUE</code>, then highlight final clusters after outlier identification. If <code>FALSE</code>, then highlight initial
clusters prior to outlier identification. Default is <code>TRUE</code>.</dd>


<dt>tp</dt>
<dd>Number between 0 and 1 to change transparency of dots in the map. Default is 1.</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>size of data points. Default value is 0.5.</dd>

</dl>

plotmap: Plotting a dimensional reduction representation

Description

Usage

Value

Arguments