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After doing a singular value decomposition (SVD) of a data set, I'm left with three matrices: 1. An orthogonal Left Singular Vector (U) 2. diagonal matrix with elements in descending order (S) 3. An orthogonal Right Singular Vector (V)

In order to plot PC1 vs PC2, I made a scatter plot (V1:V2). V1 and V2 are first and second column of V

In order to plot a scree plot: I squared the S and plotted (i,i) element of S^2 with respect to 'i'. I was thinking that diagonal elements of S^2 will give me variance.

Am I doing this right?

EDIT 1

The background:

I'm working on analysis of multiple trajectories from Molecular Dynamics simulations and I wanted to make sure that all my trajectories are somewhat exploring similar configuration space as a control measure. I use a custom made SVD code that can take trajectory info as input. Unfortunately, this data type is not compatible with R like programs without further effort. But the code that I'm using already spits out LSV, RSV and diagonal matrices after SVD.

I can rephrase the question as below : Can I take the square of diagonal elements of (S) matrix as variance so that I can use it as the y axis of the scree plot. Given that both my LSV and RSV are orthogonal.

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  • $\begingroup$ Programs that do principal component analysis ought to print the scree plot for you. Certainly SAS and R can do so. Any program that does not ... well, maybe you should switch to a better program. $\endgroup$ – Peter Flom - Reinstate Monica Jul 28 at 12:01
  • $\begingroup$ Hi @PeterFlom I have provided more info about my background. $\endgroup$ – AshlinJP Jul 28 at 17:26

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