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

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

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')

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