plotPT

Highlight clusters or pseudotime in dimensional reduction representation and indicate trajectory derived by slingshot.

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

plotPT function

<dl><dt>pt</dt>
<dd>List object returned by function <code>pseudoTime</code>.</dd>
<dt>object</dt>
<dd>RaceID <code>SCseq</code> object.</dd>
<dt>clusters</dt>
<dd>logical. If <code>TRUE</code>, then clusters are highlighted. Otherwise, pseudotime is highlighted. Default is <code>TRUE</code>.</dd>
<dt>lineages</dt>
<dd>logical. If <code>TRUE</code>, then lineages as linear connections of clusters are hghlighted. Otherwise, continuous trajectories are shown. Default is <code>FALSE</code>.</dd></dl>

Arguments

Plotting pseudo-time in dimensional reduction representation — plotPT

<dl>

<dt>pt</dt>
<dd>List object returned by function <code>pseudoTime</code>.</dd>


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


<dt>clusters</dt>
<dd>logical. If <code>TRUE</code>, then clusters are highlighted. Otherwise, pseudotime is highlighted. Default is <code>TRUE</code>.</dd>


<dt>lineages</dt>
<dd>logical. If <code>TRUE</code>, then lineages as linear connections of clusters are hghlighted. Otherwise, continuous trajectories are shown. Default is <code>FALSE</code>.</dd>

</dl>

plotPT: Plotting pseudo-time in dimensional reduction representation

Description

Usage

Value

Arguments