Add matrix section of merged objects docs page

[sjspielman]

Towards #219

This PR establishes a merged_objects.md documentation page, to be listed right after sce_file_contents.md. To begin, I have written opening sections for both SCE and AnnData objects about accessing matrices. Along the way, I also made some associated change in the "mirrored" sections of sce_file_contents.md.

I figure this page is best handled via a couple stacked PRs to avoid docs review fatigue! So, expect a couple more after this.

During review, let me know if I went too far and/or not far enough with some of these changes, and of course any wording reviews for the merged object version! These are the particular additions I made:

• In the sce_file_contents.md, we needed to also mention logcounts so I added that wording and code
• I added code for accessing column/row names for the matrices. We mentioned the row/column names but we did not show how to access them.
• I added code for accessing the spliced matrix, which may not be obvious since you have to use assay().
  • I'm not actually sure what the right code is to pull out this matrix in the AnnData object. It appears to be there, if I'm interpreting layers: 'logcounts', 'spliced' correctly? Any guidance here on how to do things in python would be great!

[sjspielman]

Thanks for the useful feedback @allyhawkins! I definitely needed a lot more (or like, any...) emphasis that merged objects are in fact merged. I have rephrased the areas as requested, and I included a little extra language in the overall intro - lmk what you think should be kept and what should be discarded!

[sjspielman]

I'm not actually sure what the right code is to pull out this matrix in the AnnData object. It appears to be there, if I'm interpreting layers: 'logcounts', 'spliced' correctly? Any guidance here on how to do things in python would be great!

Also excited to not have to figure this out 😉