mdsPlottly: mdsPlottly

In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis

mdsPlottly

Description

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

Usage

mdsPlottly(x, Sample, Group, title, palette, top, gene.selection)

Arguments

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

Details

This function computes multidimensional scaling (MDS) coordinates with limma's "plotMDS() " and then renders an interactive scatterplot via "plotly::ggplotly() ".

1. Compute MDS on the input data with "limma::plotMDS() ".

2. Extract eigenvalues and first two dimensions for variance annotation.

3. Build a ggplot2 scatterplot with axis labels showing percent variance explained.

4. Convert the ggplot to an interactive Plotly graph.

Value

A Plotly object ( "plotly::ggplotly ") representing the interactive MDS scatterplot.

inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.