plotSampleRelation {lumi} | R Documentation |
plot the sample relations based on MDS or hierarchical clustering
plotSampleRelation(x, selProbe = NULL, cv.Th = 0.1, standardize = TRUE, method = c("cluster", "mds"), dimension = c(1, 2), color = NULL)
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 |
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.
Plot the results or return the distance matrix.
Pan Du
lumiQ
, LumiBatch
, , plot.LumiBatch
## 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')