Seurat (version 2.1.0)

GetCentroids: Get cell centroids

Description

Calculate the spatial mapping centroids for each cell, based on previously calculated mapping probabilities for each bin.

Usage

GetCentroids(object, cells.use = NULL, get.exact = TRUE)

Arguments

object

Seurat object

cells.use

Cells to calculate centroids for (default is all cells)

get.exact

Get exact centroid (Default is TRUE). If FALSE, identify the single closest bin.

Value

Data frame containing the x and y coordinates for each cell centroid.

Details

Currently, Seurat assumes that the tissue of interest has an 8x8 bin structure. This will be broadened in a future release.

Examples

# NOT RUN {
# Note that the PBMC test example object does not contain spatially restricted
# examples below are only demonstrate code
pmbc_small <- GetCentroids(pbmc_small, cells.use=[e-mail])
# }
# NOT RUN {
# }