make_conn_mat: Make connectivity matrix

In soymintc/scBSC: Bivariate Spatial Correlation for Spatial Single Cell RNA-Seq

Description

This function calculates the connectivity of a spatial cell to other cells.

Usage

make_conn_mat(sdata, orig.ident = NULL, verbose = F)

Arguments

sdata	Seurat formatted spatial 10X scRNA expression data
orig.ident	A unique orig.ident for creating connectivity matrix.
verbose	Print intermediate value checks as stderr()

Details

Returns a list of spatial connectivity matrix variables (C, W) according to Lee S. J Geograph Syst (2001) 3:369-385.

Value

A list containing $barcodes_in_tissue (barcodes of spatial cells with 'tissue=TRUE'), $nbarcodes_in_tissue (length of barcodes_in_tissue), $C (raw connectivity/adjacency matrix), $W (row-sum divided connectivity matrix), $L_estimate_divR (L estimate, divided by Pearson's R (used later))

Examples

#' # Refer to https://github.com/soymintc/scBSC

soymintc/scBSC documentation built on Dec. 23, 2021, 4:24 a.m.