findBorderCells: Find cells at the image border

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

Find cells at the image border

Description

Detection of cells close to the image border for subsequent exclusion from downstream analyses.

Usage

findBorderCells(object, img_id, border_dist, coords = c("Pos_X", "Pos_Y"))

Arguments

object	a SingleCellExperiment or SpatialExperiment object.
img_id	single character indicating the colData(object) entry containing the unique image identifiers.
border_dist	single numeric defining the distance to the image border. The image border here is defined as the minimum and maximum among the cells' x and y location.
coords	character vector of length 2 specifying the names of the colData (for a SingleCellExperiment object) or the spatialCoords entries indicating the cells' x and y locations.

Value

an object of class(object) containing the logical border_cells entry in the colData slot.

Examples

library(cytomapper)
data("pancreasSCE")

sce <- findBorderCells(pancreasSCE, img_id = "ImageNb", 
                       border_dist = 10)

plotSpatial(sce, 
            img_id = "ImageNb", 
            node_color_by = "border_cells",
            scales = "free")

BodenmillerGroup/imcRtools documentation built on July 1, 2024, 5:15 p.m.