Description Usage Arguments Value See Also Examples
This function plots the PCA / MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.
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obj |
A MRexperiment object or count matrix. |
tran |
Transpose the matrix. |
comp |
Which components to display |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
log |
Whether or not to log2 the counts - if MRexperiment object. |
usePCA |
TRUE/FALSE whether to use PCA or MDS coordinates (TRUE is PCA). |
useDist |
TRUE/FALSE whether to calculate distances. |
distfun |
Distance function, default is stats::dist |
dist.method |
If useDist==TRUE, what method to calculate distances. |
n |
Number of features to make use of in calculating your distances. |
... |
Additional plot arguments. |
coordinates
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