lumi (version 2.24.0)

plotSampleRelation: visualize the sample relations

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.

Value

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

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.

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')