See loadings with Harman

[ashleymaeconard]

Hi! Could you tell me how I can use Harman's functionality to get the loadings for each PC? I would like to plot the explained variance in a simple histogram.

[JasonR055]

Hi there,
Internally Harman uses the R base library prcomp function for PCA. The harmanresults S3 object has 7 slots, one of which is rotation. These are the loadings of the original PCA. For an explanation of the prcomp slots, this is worth a read.

What Harman modifies is the scores, or the x slot in prcomp. It renames the x slot as original and places the new set of batch corrected scores in the corrected slot. The loadings should remain static. To verify, you could run prcomp or princomp on the original and reconstructed data.

Also, if you're not, please use the Harman build in Bioconductor and not github. I haven't been updating the github code that often.

Thanks for using Harman,
Jason