Don't take the transpose of count JSON data

[fedarko]

Currently, we expect the counts data to be organized something like

{Feature 1: {Sample 1: ... }}, instead of the other way around. But the default .to_dict() call on the table DF does things the other way, giving us {Sample 1: {Feature 1: ... }}.

It shouldn't really make that huge of a difference in the JS / testing sides of things, but changing this will require a lot of small modifications to various files. (That being said it will make the python script (slightly?) faster, so that's nice!)