generateMaskSeurat: Generates mask from a Seurat object. Requires 'SeuratObject'...

In mascarade: Generating Cluster Masks for Single-Cell Dimensional Reduction Plots

Generates mask from a Seurat object. Requires SeuratObject package.

Description

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))
}

mascarade documentation built on March 7, 2026, 1:07 a.m.