mdsplot.RGset: MDS (MultiDimensional Scaling) Plots

In hbc/CHBUtils: "Useful utility functions used at the core"

Description

MDS (MultiDimensional Scaling) Plots

Usage

mdsplot.RGset(dat, numPositions = 1000, sampGroups, sampNames,
  main = "MDS plot", alpha = 1, cex = 1)

Arguments

dat	object, RGChannelSet, required
numPositions,	integer, number of most variable positions to use for MDS, defaults to 1000
sampGroups,	chracter string, column name in phenoData of RGset containing groups for coloring groups on plot, required
sampNames,	chracter string , column name in phenoData of RGset containing sample labels for plot, optional
main	chracter string, title for the plot, defaults to "MDSplot"
alpha	floating point, alpha shading from 0 (transparent) to 1 (opaque), defaults to 1
cex	integer, size of points in plot, defaults to 1

Value

plot of samples plotted by MDS

See Also

cmdscale which this function uses to calculate MDS

Examples

mdsplot.RGset(dat=RGset, numPositions=1000, sampGroups="groups", sampNames="sampleIDs", main="MDSplot", alpha=0.8, cex=10)

hbc/CHBUtils documentation built on May 17, 2019, 3:07 p.m.