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?
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.