SignacX (version 2.2.5)

CID.GetDistMat: Computes distance matrix from edge list

Description

CID.GetDistMat returns the distance matrix (i.e., adjacency matrix, second-degree adjacency matrix, ..., etc.) from an edge list. Here, edges is the edge list, and n is the order of the connetions.

Usage

CID.GetDistMat(edges, n = 4)

Arguments

edges

a data frame with two columns; V1 and V2, specifying the cell-cell edge list for the network

n

maximum network distance to subtend (n neighbors)

Value

adjacency matrices for distances < n

Examples

# NOT RUN {
# Loads edges
file.dir = "https://kleintools.hms.harvard.edu/tools/client_datasets/"
file = "CITESEQ_EXPLORATORY_CITESEQ_5K_PBMCS/FullDataset_v1_protein/edges.csv"
download.file(paste0(file.dir, file, "?raw=true"), destfile = "edges.csv")

# data.dir is your path to the "edges.csv" file
edges = CID.LoadEdges(data.dir = ".")

# get distance matrix (adjacency matrices with up to fourth-order connections) from edge list
distance_matrices = CID.GetDistMat(edges)
# }