calc_distance: Distance calculations for spatial coord

In NCBI-Hackathons/RClusterCT: Classifier for Single-cell RNA-seq Using Cell Clusters

Distance calculations for spatial coord

Description

Distance calculations for spatial coord

Usage

calc_distance(
  coord,
  metadata,
  cluster_col = "cluster",
  collapse_to_cluster = FALSE
)

Arguments

coord	dataframe or matrix of spatial coordinates, cell barcode as rownames
metadata	data.frame or vector containing cluster assignments per cell. Order must match column order in supplied matrix. If a data.frame provide the cluster_col parameters.
cluster_col	column in metadata with cluster number
collapse_to_cluster	instead of reporting min distance to cluster per cell, summarize to cluster level

Value

min distance matrix

Examples

cbs <- paste0("cb_", 1:100)

spatial_coords <- data.frame(row.names = cbs,
                             X = runif(100),
                             Y = runif(100))
group_ids <- sample(c("A", "B"), 100, replace = TRUE)
dist_res <- calc_distance(
    spatial_coords, 
    group_ids
)

NCBI-Hackathons/RClusterCT documentation built on April 8, 2024, 4:36 a.m.