knn-graph

Create a kNN-graph from a high-dimensional dataset to visualize each point's nearest neighbors.

kNNGraph_script.R can be used to generate a network of nearest neighbors with minimal user input. An example is loaded using SCoPE2 data from Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity in which proteomes of single monocytes and macrophage cells are quantified relative to each other. Using a kNN-graph we can visualize the heterogeneity that exists within a cell-type, and in a future patch, investigate clustering by using gradient coloring to indicate the differential abundance of features (e.g. the enrichment of a specific protein or GO-term)

To run an example:

1. Download the SCoPE2_processed_data.csv and kNNGraph_script.R files
2. Run the kNNGraph_script.R file and it should generate a k-nearest-neighbor network as a .html.

To run a user-specific dataset:

1. Organize a matrix with row names indicating the identity of each future node (e.g. cell-type) and column names indicating the identity of each feature (e.g. protein abundance).
2. At the top of kNNGraph_script.R, set your data path, and specify the names by which to group and color the nodes.