plotSampleRelation: visualize the sample relations

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

plot the sample relations based on MDS or hierarchical clustering

Usage

plotSampleRelation(x, subset = NULL, cv.Th = 0.1, standardize = TRUE, method = c("cluster", "mds"), dimension = c(1, 2), color = NULL, main = NULL, pch=NULL, addLegend=TRUE, ...)

Arguments

x	a LumiBatch object, ExpressionSet object or a matrix with each column corresponding to a sample
subset	the subset probes used to determine the sample relations. If it is one number, then randomly selected "number" of probes will be used. If not provide, all the probes will be used.
cv.Th	the threshold of the coefficient of variance of probes used to select probes to estimate sample relations
standardize	standardize the expression profiles or not
method	"MDS" or "hierarchical clustering"
dimension	the principle components to visualize the MDS plot
color	the color for each sample during plot. Only support the "mds" method
main	the title of the plot
pch	use symbols instead of text to label the samples
addLegend	Whether to add legend to MDS (two-dimensional PCA) plot
...	Other parameters used by plot function.

Details

Estimate the sample relations based on selected probes (based on large coefficient of variance (mean / standard variance)). Two methods can be used: MDS (Multi-Dimensional Scaling) or hierarchical clustering methods.

Value

Invisibly return the hierarchical clustering results (if 'cluster' method used) or coordinates of the mds plot (if 'mds' method used) .

Author(s)

Pan Du

See Also

lumiQ, LumiBatch, , plot,ExpressionSet-method

Examples

## load example data
data(example.lumi)

## plot the sample relations with MDS
## the color of sample is automatically set based on the sample type
plotSampleRelation(example.lumi, col=c('100US', '95US:5P', '100US', '95US:5P'))

## plot the sample relations with hierarchical clustering
plotSampleRelation(example.lumi, method='cluster')

lumi documentation built on Nov. 8, 2020, 5:27 p.m.