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

data("exampleSeurat")

maskTable <- generateMaskSeurat(exampleSeurat)

library(ggplot2)
Seurat::DimPlot(exampleSeurat) +
    geom_path(data=maskTable, aes(x=UMAP_1, y=UMAP_2, group=group)) +
    coord_fixed()