plotspantree

This function plots a minimum spanning tree of the RaceID3 cluster medoids in a two-dimensional reduction representation.

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

plotspantree function

<dl><dt>object</dt>
<dd><code>Ltree</code> class object.</dd>
<dt>tp</dt>
<dd>Real number between zero and one. Level of transparency of the t-SNE map. Deafault is 0.5.</dd>
<dt>cex</dt>
<dd>real positive number. Size of data points. Deault is 1.</dd>
<dt>projections</dt>
<dd>logical. If <code>TRUE</code>, then the projections of the cells onto the inter-medoid links as computed by StemID
are shown. Default is <code>FALSE</code></dd></dl>

Arguments

Minimum Spanning Tree of RaceID3 clusters — plotspantree

<dl>

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


<dt>tp</dt>
<dd>Real number between zero and one. Level of transparency of the t-SNE map. Deafault is 0.5.</dd>


<dt>cex</dt>
<dd>real positive number. Size of data points. Deault is 1.</dd>


<dt>projections</dt>
<dd>logical. If <code>TRUE</code>, then the projections of the cells onto the inter-medoid links as computed by StemID
are shown. Default is <code>FALSE</code></dd>

</dl>

plotspantree: Minimum Spanning Tree of RaceID3 clusters

Description

Usage

Value

Arguments