Plot a metadata selection in a biaxial FeatureScatter plot

Usage

BackgatePlot(
  object,
  feature1,
  feature2,
  metadata.col,
  metadata.selection,
  assay = "RNA",
  layer = "data",
  label.cols = c("red", "grey"),
  pt.size = 1,
  add.density = FALSE,
  density.col = "black",
  noise.zero = FALSE,
  noise.zero.bound = -0.01,
  raster = TRUE,
  raster.dpi = c(512, 512)
)

Arguments

object: Seurat object
feature1: The x-axis feature
feature2: The y-axis feature
metadata.col: The column within the object meta.data to select from
metadata.selection: The entry within metadata.col to highlight
assay: Which assay
layer: Which layer in the assay, typically data
label.cols: 2-d vector specifying colors for labelling
pt.size: Size of geom_point
add.density: Whether to add geom_density_2d estimation to figure
density.col: The color of the density contour (if added)
noise.zero: Whether to simulate values from 0 to a negative value, done for visual purposes ONLY and for kernel density estimation when overlaying a density visualization. Will simulate values using a normal distribution centered at 0, take absolute values, and then scale from noise.zero.bound to 0.
noise.zero.bound: The negative value to which to simulate zeros to.
high.p: Which percentile to set as 1

Value

Returns a Seurat object with scaled values in the data layer of the specified assay

Details

Scales the expression values for each feature in the specified assay from 0 to 1, with an optional split.by argument