plotgraph

This function plots a graph of lineage trajectories connecting RaceID3 cluster medoids as inferred by StemID2 to approximate the lineage tree. The plot
highlights significant links, where colour indicates the level of significance and width indicates the link score. The node colour reflects the level
of transcriptome entropy.

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

plotgraph function

<dl><dt>object</dt>
<dd><code>Ltree</code> class object.</dd>
<dt>showCells</dt>
<dd>logical. If <code>TRUE</code>, then projections of cells are shown in the plot. Default is <code>FALSE</code>.</dd>
<dt>showMap</dt>
<dd>logical. Tf <code>TRUE</code>, then show transparent t-SNE map (with transparency <code>tp</code>) of cells in the background. Default is <code>TRUE</code>.</dd>
<dt>tp</dt>
<dd>Real number between zero and one. Level of transparency of the t-SNE map. Deafault is 0.5. See <code>showMap</code>.</dd>
<dt>scthr</dt>
<dd>Real number between zero and one. Score threshold for links to be shown in the graph. For <code>scthr=0</code> all significant links are shown.
The maximum score is one. Default is 0.</dd>
<dt>cex</dt>
<dd>real positive number. Size of data points. Deault is 1.</dd></dl>

Arguments

StemID2 Lineage Graph — plotgraph

<dl>

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


<dt>showCells</dt>
<dd>logical. If <code>TRUE</code>, then projections of cells are shown in the plot. Default is <code>FALSE</code>.</dd>


<dt>showMap</dt>
<dd>logical. Tf <code>TRUE</code>, then show transparent t-SNE map (with transparency <code>tp</code>) of cells in the background. Default is <code>TRUE</code>.</dd>


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


<dt>scthr</dt>
<dd>Real number between zero and one. Score threshold for links to be shown in the graph. For <code>scthr=0</code> all significant links are shown.
The maximum score is one. Default is 0.</dd>


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

</dl>

plotgraph: StemID2 Lineage Graph

Description

Usage

Value

Arguments