How do I generate a PLSDA/VIP plot for RNA-seq data generated in DESeq2?

I have conducted some RNA seq analysis using DESeq2 software in R. I want to gain an understanding of what is driving the clustering of samples in the principle components plot. I wanted to to Variable importance Plot or PLSDA but I saw a post saying that because it is a linear model the order of variables included in the design would affect how much they contributed to clustering. What if I included only the variable of interest and then no cofactors is there a way to explore the contribution of other variables then? I'm new to RNA seq analysis so apologies if I have confused myself and am stuck down an side road here! (Note I have already generated a loadings plot and it didn't give me enough of an answer to my question).