MDSPlot: MDS plot (for edgeR objects)

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

MDS plot (for edgeR objects)

Description

Multi-Dimensional Scaling plot of samples based on the 500 most variant features (for edgeR analyses)

Usage

MDSPlot(
  dge,
  group,
  n = min(500, nrow(dge$counts)),
  gene.selection = c("pairwise", "common"),
  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"),
  outfile = TRUE,
  ggplot_theme = theme_gray()
)

Arguments

dge	a DGEList object
group	vector of the condition from which each sample belongs
n	number of features to keep among the most variant
gene.selection	"pairwise" to choose the top features separately for each pairwise comparison between the samples or "common" to select the same features for all comparisons. Only used when method="logFC"
col	colors to use (one per biological condition)
outfile	TRUE to export the figure in a png file
ggplot_theme	ggplot2 theme function (theme_gray() by default)

Value

A file named MDS.png in the figures directory

Author(s)

Marie-Agnes Dillies and Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.