clustheatmap

This functions plots a heatmap of the distance matrix grouped by 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

clustheatmap function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>final</dt>
<dd>logical. If <code>TRUE</code>, then cells are grouped based on final clusters after outlier identification.
If <code>FALSE</code>, then initial clusters prior to outlier identification are used for grouping. Default is <code>TRUE</code>.</dd>
<dt>hmethod</dt>
<dd>Agglomeration method used for determining the cluster order from hierarchical clustering of the cluster medoids. See <code>hclust</code> function.</dd></dl>

Arguments

Plotting a Heatmap of the Distance Matrix — clustheatmap

<dl>

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


<dt>final</dt>
<dd>logical. If <code>TRUE</code>, then cells are grouped based on final clusters after outlier identification.
If <code>FALSE</code>, then initial clusters prior to outlier identification are used for grouping. Default is <code>TRUE</code>.</dd>


<dt>hmethod</dt>
<dd>Agglomeration method used for determining the cluster order from hierarchical clustering of the cluster medoids. See <code>hclust</code> function.</dd>

</dl>

clustheatmap: Plotting a Heatmap of the Distance Matrix

Description

Usage

Value

Arguments