Generate a multidimensional scaling (MDS) plot based on expression data.
mdsPlot(
x,
Sample,
Group,
title,
palette,
maxOverlaps,
sizeLabel,
top,
gene.selection
)A "ggplot " object representing the MDS plot.
DGEList object from edgeR.
A character vector of sample labels (one per column in "x ").
A factor or character vector specifying the group/class of each sample.
Plot title as a character string.
Name of a palette from the "paletteer " package for coloring groups.
Maximum number of overlapping labels allowed by "geom_text_repel ".
Numeric value for label font size.
Integer. Number of top most variable genes to include in MDS.
Method for gene selection: one of "pairwise", "common", or "logFC".
This function performs MDS analysis using limma's "plotMDS() " and visualizes the sample relationships in two dimensions using "ggplot2 " and "ggrepel ".