violinMarkerPlot

Displaying violin plots of gene expression or gene expression noise (epsilon) across (a set of) 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

violinMarkerPlot function

<dl><dt>g</dt>
<dd>Valid gene ID corresponding to a (set of) rownames of <code>object@ndata</code> or <code>noise</code>.</dd>
<dt>object</dt>
<dd>RaceID <code>SCseq</code> object.</dd>
<dt>noise</dt>
<dd>List of noise parameters returned by <code>compTBNoise</code>. If this argument is given, then the distribution of noise (epsilon) is plotted. Default is NULL and normalized gene expression (normalized by median count across all clusters in <code>set</code>) is plotted.</dd>
<dt>set</dt>
<dd>Postive integer number or vector of integers corresponding to valid cluster numbers. Violin plots are shown for all clusters in <code>set</code>. Default is NULL and data are shown for all clusters in <code>object@cpart</code>.</dd>
<dt>ti</dt>
<dd>String of characters representing the title of the plot. Default is <code>NULL</code> and the first element of <code>g</code> is chosen.</dd></dl>

Arguments

Violin plot of marker gene expression or noise — violinMarkerPlot

<dl>

<dt>g</dt>
<dd>Valid gene ID corresponding to a (set of) rownames of <code>object@ndata</code> or <code>noise</code>.</dd>


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


<dt>noise</dt>
<dd>List of noise parameters returned by <code>compTBNoise</code>. If this argument is given, then the distribution of noise (epsilon) is plotted. Default is NULL and normalized gene expression (normalized by median count across all clusters in <code>set</code>) is plotted.</dd>


<dt>set</dt>
<dd>Postive integer number or vector of integers corresponding to valid cluster numbers. Violin plots are shown for all clusters in <code>set</code>. Default is NULL and data are shown for all clusters in <code>object@cpart</code>.</dd>


<dt>ti</dt>
<dd>String of characters representing the title of the plot. Default is <code>NULL</code> and the first element of <code>g</code> is chosen.</dd>

</dl>

violinMarkerPlot: Violin plot of marker gene expression or noise

Description

Usage

Value

Arguments