Updates to AnnData contents based on new scanpy compatibility

[allyhawkins]

Closes #337

Related to changes described in https://github.com/AlexsLemonade/scpca-nf/issues/773 and made in https://github.com/AlexsLemonade/scpca-nf/pull/774.

Here I'm accounting for the new changes to contents in the individual and merged AnnData objects. Both objects have the following changes:

• X_PCA and X_UMAP have been renamed to X_pca and X_umap
• highly_variable is now a column in the .var slot indicating if a gene is part of the HVG list

Just the individual objects will have:

• A new .uns["pca"] object that contains information about parameters and variance for PCA. I didn't describe every element of this, because I think if someone is using it they know what they're doing. Let me know if the explanation that I included is okay or if I should add more detail.

I made the changes in the SCE contents file (in the AnnData section) and the merged object file. I think that should be everything.

[allyhawkins]

Thanks for catching that! I updated the PCA/UMAP names in the getting started doc, and I added a small sentence about the highly variable column. I'm still 50/50 on if we need it, but I don't think it can hurt. @sjspielman can you take a look at that change in https://github.com/AlexsLemonade/scpca-docs/pull/338/commits/f16c8b0e75f21d38b7cdbb0f421a499c1bcb2d9a.