Plot classical MDS of dataset — plotCMDS • netZooR

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