generateMask: Generate mask for clusters on 2D dimensional reduction plots

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

Generate mask for clusters on 2D dimensional reduction plots

Description

Internally the function rasterizes and smoothes the density plots.

Usage

generateMask(
  dims,
  clusters,
  gridSize = 200,
  expand = 0.005,
  minDensity = lifecycle::deprecated(),
  smoothSigma = NA,
  minSize = 10,
  kernel = lifecycle::deprecated(),
  type = lifecycle::deprecated()
)

Arguments

dims	matrix of point coordinates. Rows are points, columns are dimensions. Only the first two columns are used.
clusters	vector of cluster annotations. Should be the same length as the number of rows in dims.
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.
minDensity	Deprecated. Doesn't do anything.
smoothSigma	Deprecated. Parameter controlling smoothing and joining close cells into groups, represented as a fraction of sqrt(width*height). Increasing this parameter can help dealing with sparse regions.
minSize	Groups of less than minSize points are ignored, unless it is the only group for a cluster
kernel	Deprecated. Doesn't do anything.
type	Deprecated. Doesn't do anything.

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("exampleMascarade")
maskTable <- generateMask(dims=exampleMascarade$dims,
                          clusters=exampleMascarade$clusters)
data <- data.frame(exampleMascarade$dims,
                   cluster=exampleMascarade$clusters,
                   exampleMascarade$features)
library(ggplot2)
ggplot(data, aes(x=UMAP_1, y=UMAP_2)) +
    geom_point(aes(color=cluster)) +
    geom_path(data=maskTable, aes(group=group)) +
    coord_fixed() +
    theme_classic()

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