plotQQ

Displaying two noise-related quantaties of local pruned k-nearest neighbourhoods in a scatterplot highlighting VarID 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

plotQQ function

<dl><dt>x</dt>
<dd>List object returned by <code>quantKnn</code> function.</dd>
<dt>m</dt>
<dd>Component name of <code>x</code>. One of "noise.av", "noise.ratio", "local.corr", "umi".</dd>
<dt>n</dt>
<dd>Component name of <code>x</code>. One of "noise.av", "noise.ratio", "local.corr", "umi".</dd>
<dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>cluster</dt>
<dd>Valid cluster number or vector of cluster numbers, contained in <code>object@cpart</code>. If given, then cells of clusters in <code>cluster</code> are circled in black.</dd>
<dt>cex</dt>
<dd>Real positive number. Size of data points. Default is 0.5.</dd>
<dt>show.cor</dt>
<dd>logical. If <code>TRUE</code> then Pearson's correlation is shown in the legend. Default is <code>TRUE</code>.</dd>
<dt>...</dt>
<dd>Additional parameters of <code>plot</code> (e.g., <code>log</code>, see <code><a href="/link/help(plot)?package=RaceID&version=0.3.9" data-mini-rdoc="RaceID::help(plot)">help(plot)</a></code>).</dd></dl>

Arguments

Scatter plot of two noise-related quantaties of local pruned k-nearest neighbourhoods — plotQQ

<dl>

<dt>x</dt>
<dd>List object returned by <code>quantKnn</code> function.</dd>


<dt>m</dt>
<dd>Component name of <code>x</code>. One of "noise.av", "noise.ratio", "local.corr", "umi".</dd>


<dt>n</dt>
<dd>Component name of <code>x</code>. One of "noise.av", "noise.ratio", "local.corr", "umi".</dd>


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


<dt>cluster</dt>
<dd>Valid cluster number or vector of cluster numbers, contained in <code>object@cpart</code>. If given, then cells of clusters in <code>cluster</code> are circled in black.</dd>


<dt>cex</dt>
<dd>Real positive number. Size of data points. Default is 0.5.</dd>


<dt>show.cor</dt>
<dd>logical. If <code>TRUE</code> then Pearson's correlation is shown in the legend. Default is <code>TRUE</code>.</dd>


<dt>...</dt>
<dd>Additional parameters of <code>plot</code> (e.g., <code>log</code>, see <code><a href='https://rdrr.io/r/graphics/plot.default.html'>help(plot)</a></code>).</dd>

</dl>

plotQQ: Scatter plot of two noise-related quantaties of local pruned k-nearest neighbourhoods

Description

Usage

Value

Arguments