getproj

This function extracts projections of all cells in a cluster and plots a heatmap of these hierarchically clustered projections (rows)
to all other clusters (columns). A minimum spanning tree of the cluster centers is overlaid for comparison.

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

getproj function

<dl><dt>object</dt>
<dd><code>Ltree</code> class object.</dd>
<dt>i</dt>
<dd>Cluster number. This number has to correspond to one of the RaceID3 clusters included for the StemID2 inference, i.e. to a number present
in slot <code>ldata$lp</code>.</dd>
<dt>show</dt>
<dd>logical. If <code>TRUE</code>, then plot heatmap of projections. Default is <code>TRUE</code>.</dd>
<dt>zscore</dt>
<dd>logical. If <code>TRUE</code> and <code>show=TRUE</code>, then plot z-score-transformed projections. If <code>TRUE</code> and <code>show=FALSE</code>,
then plot untransformed projections. Default is <code>FALSE</code>.</dd></dl>

Arguments

Extract Projections of all Cells from a Cluster — getproj

<dl>

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


<dt>i</dt>
<dd>Cluster number. This number has to correspond to one of the RaceID3 clusters included for the StemID2 inference, i.e. to a number present
in slot <code>ldata$lp</code>.</dd>


<dt>show</dt>
<dd>logical. If <code>TRUE</code>, then plot heatmap of projections. Default is <code>TRUE</code>.</dd>


<dt>zscore</dt>
<dd>logical. If <code>TRUE</code> and <code>show=TRUE</code>, then plot z-score-transformed projections. If <code>TRUE</code> and <code>show=FALSE</code>,
then plot untransformed projections. Default is <code>FALSE</code>.</dd>

</dl>

getproj: Extract Projections of all Cells from a Cluster

Description

Usage

Value

Arguments