plotCMDS: Plot classical MDS of dataset

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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 May 8, 2019, 3:49 a.m.