Which data source is used for plot_pca?

[thorellk]

Hi!

I am trying to recreate the pca plots generated by the sleuth plot_pca function with ggplot so that I can use more aesthetics functions but I cannot find out what of the sleuth object data the plot_pca function uses. I have looked into the code in detail and found that you use a custom function called spread_abundance_by but trying to use this gives me errors and I am not enough of an R-wiz to get any further, I think. I have tried to use the sleuth_to_matrix function but it gives me slightly different results.

Best wishes, Kaisa