plotMV

This functions plots the dependence of the transcript count variance or, alternatively, the coefficient of variation (CV) on the mean in log2 space. The mean-variance dependence is plotted along with a loess-regression, a second order polynomial fit, and the background model of the local variability. The CV plot also highlights the local variability associated with cell-to-cell variability of total transcript counts, as calculated directly from the mean and variance of total transcript counts (turquoise) or from a local fit of a gamma distribution (orange).

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

plotMV function

<dl><dt>x</dt>
<dd>Transcript count matrix.</dd>
<dt>cv</dt>
<dd>Logical. If <code>TRUE</code> then the coefficient of variation is plotted instead of the variance. Default is <code>FALSE</code>.</dd>
<dt>ret</dt>
<dd>Logical. If <code>TRUE</code> then a second order polynomial fit is returned. Default is <code>FALSE</code></dd>
<dt>span</dt>
<dd>Parameter for the local regression. See help(loess). Default value is 0.75.</dd>
<dt>degree</dt>
<dd>Parameter for the local regression. See help(loess). Default value is 2.</dd>
<dt>...</dt>
<dd>Additional arguments for <code>plot</code>.</dd></dl>

Arguments

Plot of Mean-Variance dependence and various fits — plotMV

<dl>

<dt>x</dt>
<dd>Transcript count matrix.</dd>


<dt>cv</dt>
<dd>Logical. If <code>TRUE</code> then the coefficient of variation is plotted instead of the variance. Default is <code>FALSE</code>.</dd>


<dt>ret</dt>
<dd>Logical. If <code>TRUE</code> then a second order polynomial fit is returned. Default is <code>FALSE</code></dd>


<dt>span</dt>
<dd>Parameter for the local regression. See help(loess). Default value is 0.75.</dd>


<dt>degree</dt>
<dd>Parameter for the local regression. See help(loess). Default value is 2.</dd>


<dt>...</dt>
<dd>Additional arguments for <code>plot</code>.</dd>

</dl>

plotMV: Plot of Mean-Variance dependence and various fits

Description

Usage

Value

Arguments