signaturePCA: Create three PCA plots for signatures.
In sjdlabgroup/MutSigTools: Mutational signature analysis

Description Usage Arguments Value See Also Examples

Constructs three PCA plots showing variations among the signatures in terms of the weights of the principal components for different mutation signatures, as well as the eigenvalues and cosine similarity among expected and actual signatures.

1	signaturePCA(sigmat, pngfile )

`sigmat`	An object of class mutsig describing a set of signatures.
`pngfile`	name of png formatted image file to be created

Create three PCA plots with the following extensions to show difference among mutational signatures.

*_Eigen.png The eigenvalues of the PCA and the relative amount of the variation each eigenvalue.
*_var.png The different single-nucleotide alteration components in terms of the two dimensions.
*_PCA.png The different signatures in terms of the 2 non-dimensional vectors derived by the PCA analysis and the cosine similarity between the estimate of each mutation signature using PCA and the actual mutation signature(in order to determine how accurately the 2 dimensions calculated by PCA represent the mutational signatures).

signatureHeatmap, signatures.cosmic, deleteSignature, renameSignature and mergeSignature.