plotdimsat

This functions plots the explained variance as a function of PCA/ICA components computed by the function <code>CCcorrect</code>. The number of components where
the change in explained variability upon adding further components approaches linear behaviour demarcates the saturation point and is highlighted in blue.

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

plotdimsat function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>change</dt>
<dd>logical. If <code>TRUE</code> then the change in explained variance is plotted. Default is <code>FALSE</code> and the explained variance is shown.</dd>
<dt>lim</dt>
<dd>Number of components included for he calculation and shown in the plot. Default is <code>NULL</code> and all components are included.</dd></dl>

Arguments

Plotting the Saturation of Explained Variance — plotdimsat

<dl>

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


<dt>change</dt>
<dd>logical. If <code>TRUE</code> then the change in explained variance is plotted. Default is <code>FALSE</code> and the explained variance is shown.</dd>


<dt>lim</dt>
<dd>Number of components included for he calculation and shown in the plot. Default is <code>NULL</code> and all components are included.</dd>

</dl>

plotdimsat: Plotting the Saturation of Explained Variance

Description

Usage

Value

Arguments