Generates mask from a Seurat object. Requires SeuratObject package.

Generates mask from a Seurat object. Requires SeuratObject package.

Usage

generateMaskSeurat(
  object,
  reduction = NULL,
  group.by = NULL,
  gridSize = 200,
  expand = 0.005,
  minSize = 10
)

Arguments

object

Seurat object

reduction

character vector specifying which reduction to use (default: DefaultDimReduc(object))

group.by

character vector specifying which field to use for clusters (default: "ident")

gridSize

target width and height of the raster used internally

expand

distance used to expand borders, represented as a fraction of sqrt(width*height). Default: 1/200.

minSize

Groups of less than minSize points are ignored, unless it is the only group for a cluster

Value

data.table with points representing the mask borders. Each individual border line corresponds to a single level of group column. Cluster assignment is in cluster column.

Examples

# only run if Seurat is installed
if (require("Seurat")) {
    data("pbmc_small")
    maskTable <- generateMaskSeurat(pbmc_small)

    library(ggplot2)
    # not the best plot, see vignettes for better examples
    DimPlot(pbmc_small) +
        geom_path(data=maskTable, aes(x=tSNE_1, y=tSNE_2, group=group))
}
#> Loading required package: Seurat
#> Loading required package: SeuratObject
#> Loading required package: sp
#> ‘SeuratObject’ was built under R 4.5.0 but the current version is
#> 4.5.3; it is recomended that you reinstall ‘SeuratObject’ as the ABI
#> for R may have changed
#> 
#> Attaching package: ‘SeuratObject’
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, t