plotB

Function to generate boxplots of a feature vector across different clusters.

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

plotB function

<dl><dt>x</dt>
<dd>Vector of real numbers.</dd>
<dt>part</dt>
<dd>Vector with cluster partition, e.g., element <code>partition</code> returned by the <code>graphCluster</code> function.</dd>
<dt>cluster</dt>
<dd>Positive integer corresponing to valid cluster number or <code>NULL</code>. If valid cluster number, then a horizontal line is drawn indicating the median value of <code>x</code> for the corresponding cluster. If <code>NULL</code> no line is drawn. Default is <code>NULL</code>.</dd>
<dt>set</dt>
<dd>Ordered set of valid cluster numbers. If <code>box</code> equals <code>TRUE</code> than data will only be plotted for these clusters in the give</dd>
<dt>...</dt>
<dd>Additional parameters of <code>boxplot</code>.</dd></dl>

Arguments

Boxplots for features across clusters — plotB

<dl>

<dt>x</dt>
<dd>Vector of real numbers.</dd>


<dt>part</dt>
<dd>Vector with cluster partition, e.g., element <code>partition</code> returned by the <code>graphCluster</code> function.</dd>


<dt>cluster</dt>
<dd>Positive integer corresponing to valid cluster number or <code>NULL</code>. If valid cluster number, then a horizontal line is drawn indicating the median value of <code>x</code> for the corresponding cluster. If <code>NULL</code> no line is drawn. Default is <code>NULL</code>.</dd>


<dt>set</dt>
<dd>Ordered set of valid cluster numbers. If <code>box</code> equals <code>TRUE</code> than data will only be plotted for these clusters in the give</dd>


<dt>...</dt>
<dd>Additional parameters of <code>boxplot</code>.</dd>

</dl>

plotB: Boxplots for features across clusters

Description

Usage

Value

Arguments