Add neighborhood diversity calculation and plotting

[dtm2451]

This PR adds a new functionality and plotters to go with it:

• calculation of diversity within cells' nearest neighbors

Motivation: Plotting such data can be VERY useful for batch effect assessment

The goal is to create 3 primary functions:

1. calcNeighborMetadataDiversity(): to perform the diversity calculations
2. dittoNeighborDiversityPlot(): to automate plotting these data using dittoDimPlot()
3. dittoNeighborDiversityHex(): to automate plotting these data using dittoDimHex()

Steps:

• create calcNeighborMetadataDiversity()
  • initial documentation
  • tests
• create dittoNeighborDiversityPlot()
  • initial documentation
  • tests
• create .default_neighbors() for backend (auto-determination of Neighbors-data to use within the user giving it)
  • Establish all dafualt neighbors graph names of Seurat
• create dittoNeighborDiversityHex()
  • initial documentation
  • tests
• Investigate methodologies for SCEs to ensure not creating too much extra work for SCE users
• Finalize documentation
• Finalize tests

[dtm2451]

This work is underway, and function and input names are all subject to potentially change until merged into devel. But as this also seems to be a major hole in the field, anyone wishing to use/test these functionality early can install from this branch with remotes::install_github("dtm2451/dittoSeq@neighbor-diversity"), then restart your R if you'd already had dittoSeq loaded.

[dtm2451]

One thing to note, and I'll aim to work this into the documentation, is that the algorithm I'm basing the calcNeighborMetadataDiversity() calculation off of made use of a NearestNeighbors calculation run specifically for this purpose that used k=sqrt(ncells). This number of neighbors may be overkill for gigantic datasets, but the important thing is that using only the 20-or-so neighbors regularly recorded after a "standard" Seurat algorithm run 1) cannot yield quite as accurate of results, and 2) negates some of the utility of using a quantile cutoff on neighbor distances due to the relative inflation of such distances.

So:

• adjust documentation to recommend running neighbors calculation with higher number of neighbors retained
• adjust defaulting to 1) warn and 2) not use the distance quantile trimming unless the number of neighbors in neighbors is at least 30.