getCenters: Makes one step coarser spot mesh

In iaaka/visutils: QC, analyse and visualize visium

Makes one step coarser spot mesh

Description

Makes one step coarser spot mesh

Usage

getCenters(coors, cstart = 0L, type = 1L, to.merge = NULL, image.name = NULL)

Arguments

coors	Seurat object or coors seu@images[.]@coordinates
cstart	column coordinate of first (in -2th row) cluster center. Numbers for 0 to 13 will give different groupings.
type	orientation of mesh, 1 or -1
to.merge	logical vector specifying spots to be merged, use v$nCount_Spatial<500 to merge spots with less than 500 UMIs. NULL is identicall to all TRUE.

Details

There are severals ways to do so in dependence on starting point, this is controlled by cstart and type parameters. Maybe some combinations of these parameters results in identicall groupings, I didn't check it properly. Anyway I would suggest to always use defaults since it should not be very important.

Value

modified spot coordinate table with group column added

Examples

c2 = getCenters(v2)
plotVisium(v2,c2$group)

iaaka/visutils documentation built on Jan. 17, 2025, 11:29 p.m.