findBorderCells {imcRtools} | R Documentation

## 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.

### Author(s)

Nils Eling (nils.eling@dqbm.uzh.ch)

### Examples

    library(cytomapper)
    data("pancreasSCE")

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

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

[Package imcRtools version 1.0.2 Index]