plotSampleRelation {lumi}R Documentation

visualize the sample relations

Description

plot the sample relations based on MDS or hierarchical clustering

Usage

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

Arguments

x a LumiBatch object, ExpressionSet object or a matrix with each column corresponding to a sample
selProbe the selected probes used to determine the sample relations. 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

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

Plot the results or return the distance matrix.

Author(s)

Pan Du

See Also

lumiQ, LumiBatch, , plot.LumiBatch

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')


[Package lumi version 1.2.0 Index]