mdsPlottly

Generate an interactive MDS plot using Plotly based on expression data.

A 'shiny' app that supports both dual and bulk RNA-seq, with the dual
RNA-seq functionality offering the flexibility to perform either a
sequential approach (where reads are mapped separately to each genome)
or a combined approach (where reads are aligned to a single merged
genome). The user-friendly interface automates the analysis process,
providing step-by-step guidance, making it easy for users to navigate
between different analysis steps, and download intermediate results
and publication-ready plots.

Carmine Fruggiero

inDAGO

A GUI for Dual and Bulk RNA-Sequencing Analysis

Gaetano Aufiero

mdsPlottly function

<dl><dt>x</dt>
<dd>A DGEList object from edgeR.</dd>
<dt>Sample</dt>
<dd>Character vector. Sample names corresponding to columns of "x ".</dd>
<dt>Group</dt>
<dd>Factor or character vector. Group or condition for each sample.</dd>
<dt>title</dt>
<dd>Character. Title for the plot.</dd>
<dt>palette</dt>
<dd>Character. Name of a discrete palette from the "paletteer " package.</dd>
<dt>top</dt>
<dd>Integer. Number of top most variable genes (by logFC) to include in MDS.</dd>
<dt>gene.selection</dt>
<dd>Character. Gene selection method: one of ""pairwise" ", ""common" ", or ""logFC" ".</dd></dl>

Arguments

mdsPlottly — mdsPlottly

<dl>

<dt>x</dt>
<dd>A DGEList object from edgeR.</dd>


<dt>Sample</dt>
<dd>Character vector. Sample names corresponding to columns of "x ".</dd>


<dt>Group</dt>
<dd>Factor or character vector. Group or condition for each sample.</dd>


<dt>title</dt>
<dd>Character. Title for the plot.</dd>


<dt>palette</dt>
<dd>Character. Name of a discrete palette from the "paletteer " package.</dd>


<dt>top</dt>
<dd>Integer. Number of top most variable genes (by logFC) to include in MDS.</dd>


<dt>gene.selection</dt>
<dd>Character. Gene selection method: one of ""pairwise" ", ""common" ", or ""logFC" ".</dd>

</dl>

mdsPlottly: mdsPlottly

Description

Usage

Value

Arguments

Details