PolyFeaturePlot: Polygon FeaturePlot

In satijalab/seurat: Tools for Single Cell Genomics

Polygon FeaturePlot

Description

Plot cells as polygons, rather than single points. Color cells by any value accessible by FetchData.

Usage

PolyFeaturePlot(
  object,
  features,
  cells = NULL,
  poly.data = "spatial",
  ncol = ceiling(x = length(x = features)/2),
  min.cutoff = 0,
  max.cutoff = NA,
  common.scale = TRUE,
  flip.coords = FALSE
)

Arguments

object	Seurat object
features	Vector of features to plot. Features can come from: An Assay feature (e.g. a gene name - "MS4A1") A column name from meta.data (e.g. mitochondrial percentage - "percent.mito") A column name from a DimReduc object corresponding to the cell embedding values (e.g. the PC 1 scores - "PC_1")
cells	Vector of cells to plot (default is all cells)
poly.data	Name of the polygon dataframe in the misc slot
ncol	Number of columns to split the plot into
min.cutoff, max.cutoff	Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')
common.scale	...
flip.coords	Flip x and y coordinates

Value

Returns a ggplot object

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.