plotCMDS: Plot classical MDS of dataset

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Plot classical MDS of dataset

Description

This function plots the MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.

Usage

plotCMDS(obj, comp = 1:2, normalized = FALSE, distFun = dist,
  distMethod = "euclidian", n = NULL, samples = TRUE, log = TRUE,
  plotFlag = TRUE, ...)

Arguments

obj	ExpressionSet object or objrix.
comp	Which components to display.
normalized	TRUE / FALSE, use the normalized matrix or raw counts.
distFun	Distance function, default is dist.
distMethod	The distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given.
n	Number of features to make use of in calculating your distances.
samples	Perform on samples or genes.
log	TRUE/FALSE log2-transform raw counts.
plotFlag	TRUE/FALSE whether to plot or not.
...	Additional plot arguments.

Value

coordinates

Examples

data(skin)
res <- plotCMDS(skin,pch=21,bg=factor(pData(skin)$SMTSD))

# library(calibrate)
# textxy(X=res[,1],Y=res[,2],labs=rownames(res))

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.