mdsPlot: mdsPlot

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

mdsPlot

Description

Generate a multidimensional scaling (MDS) plot based on expression data.

Usage

mdsPlot(
  x,
  Sample,
  Group,
  title,
  palette,
  maxOverlaps,
  sizeLabel,
  top,
  gene.selection
)

Arguments

x	DGEList object from edgeR.
Sample	A character vector of sample labels (one per column in "x ").
Group	A factor or character vector specifying the group/class of each sample.
title	Plot title as a character string.
palette	Name of a palette from the "paletteer " package for coloring groups.
maxOverlaps	Maximum number of overlapping labels allowed by "geom_text_repel ".
sizeLabel	Numeric value for label font size.
top	Integer. Number of top most variable genes to include in MDS.
gene.selection	Method for gene selection: one of "pairwise", "common", or "logFC".

Details

This function performs MDS analysis using limma's "plotMDS() " and visualizes the sample relationships in two dimensions using "ggplot2 " and "ggrepel ".

Value

A "ggplot " object representing the MDS plot.

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