Initial commit of phenotype by neighbour analysis

[khoulahan]

What is the purpose of this PR?
Closes #941.
How is the phenotype of a cell impact by its neighboring cells? Addressing this question requires characterizing the neighbors of a cell. What is the average distance of the cell in question to cancer cells? Immune cells? Fibroblasts? Do these distances inform on the phenotype of the cell in question? The goal of this function is to provide per cell measurements of the median distance to the N nearest cells of each cell cluster.

How did you implement your changes

The end result is a cell by cell cluster matrix populated with the median distance to the N nearest cells of each cell cluster. The analysis is split into two functions:

1. All cells vs one cell cluster:

• For all cells of a specified cell cluster, calculates median distance to nearest N neighbours of all other cell types
• Takes four required inputs: distance matrix, cell table, cell cluster, N nearest neighbors

2. All cells vs all cell clusters

• Wrapper function that calls function 1 for all cell clusters
• Takes three required inputs: distance matrix, cell table, N nearest neighbours

Results

• Cells with closest average distance to Mono_mac cells

• Cells with farthest average distance to Mono_mac cells

[ngreenwald]

Thanks @khoulahan! I'll let you know once we've got some results

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[srivarra]

Looks good, just some stylistic stuff.

[alex-l-kong]

Just a few minor comments.

[ngreenwald]

Looks good, see below

[ngreenwald]

Looks good