PlotMBpca

The PCA representation can either be used to show pseudo-time
ordering or the gene expression of a particular gene.

An open, multi-algorithmic pipeline for easy, fast and efficient
analysis of cellular sub-populations and the molecular signatures that
characterize them. The pipeline consists of four successive steps: data
pre-processing, cellular clustering with pseudo-temporal ordering, defining
differential expressed genes and biomarker identification. More details on
Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements
extensions of the work published by Ghannoum et. al. (2019)
<doi:10.1101/700989>.

Waldir Leoncio

DIscBIO

A User-Friendly Pipeline for Biomarker Discovery in Single-Cell
Transcriptomics

Salim Ghannoum

Alvaro Köhn-Luque

Damiano Fantini

PlotMBpca function

<dl><dt>object</dt>
<dd><code>DISCBIO</code> class object.</dd>
<dt>type</dt>
<dd>either `order` to plot pseudo-time ordering or `exp` to plot gene
expression</dd>
<dt>g</dt>
<dd>Individual gene name or vector with a group of gene names
corresponding to a subset of valid row names of the <code>ndata</code> slot of
the <code>DISCBIO</code> object. Ignored if `type="order"`.</dd>
<dt>n</dt>
<dd>String of characters representing the title of the plot. Default is
NULL and the first element of <code>g</code> is chosen. Ignored if
`type="order"`.</dd></dl>

Arguments

Plotting pseudo-time ordering or gene expression in Model-based
clustering in PCA — PlotMBpca

<dl>

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


<dt>type</dt>
<dd>either `order` to plot pseudo-time ordering or `exp` to plot gene
expression</dd>


<dt>g</dt>
<dd>Individual gene name or vector with a group of gene names
corresponding to a subset of valid row names of the <code>ndata</code> slot of
the <code>DISCBIO</code> object. Ignored if `type="order"`.</dd>


<dt>n</dt>
<dd>String of characters representing the title of the plot. Default is
NULL and the first element of <code>g</code> is chosen. Ignored if
`type="order"`.</dd>

</dl>

PlotMBpca: Plotting pseudo-time ordering or gene expression in Model-based clustering in PCA

Description

Usage

Value

Arguments