barplotgene

This functions generates a barplot of gene expression across all 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

barplotgene function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>g</dt>
<dd>Individual gene name or vector with a group of gene names corresponding to a subset of valid row names of the <code>ndata</code> slot
of the <code>SCseq</code> object.</dd>
<dt>n</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>
<dt>logsc</dt>
<dd>logical. If <code>TRUE</code>, then gene expression values are log2-transformed after adding a pseudo-count of 0.1. Default is <code>FALSE</code>
and untransformed values are shown.</dd></dl>

Arguments

Gene Expression Barplot — barplotgene

<dl>

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


<dt>g</dt>
<dd>Individual gene name or vector with a group of gene names corresponding to a subset of valid row names of the <code>ndata</code> slot
of the <code>SCseq</code> object.</dd>


<dt>n</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>


<dt>logsc</dt>
<dd>logical. If <code>TRUE</code>, then gene expression values are log2-transformed after adding a pseudo-count of 0.1. Default is <code>FALSE</code>
and untransformed values are shown.</dd>

</dl>

barplotgene: Gene Expression Barplot

Description

Usage

Value

Arguments