produce a biplot based on sharing of information between a `prcomp`-like output and a SingleCellExperiment

produce a biplot based on sharing of information between a `prcomp`-like output and a SingleCellExperiment

filtered_biplot(
  prcomp_output,
  sce,
  sampvar = "Barcode",
  colorvar = "label.main",
  which = c(1, 2),
  nvar = 5,
  shr = 0.6,
  ...
)

Arguments

prcomp_output

instance of prcomp, as produced by, e.g., irlba::prcomp_irlba

sce

a SingleCellExperiment instance

sampvar

character(1) name of a variable in `colData(sce)` that will be used to label samples

colorvar

character(1) names of a variable in `colData(sce)` that will be used to color points

which

numeric(2), gives dimensions of `prcomp_output$x` to use for point locations

nvar

numeric(1) number of highly ranked features (by sum of squares of loadings) to use in biplot

shr

numeric(1) a fudge factor to 'shrink' projection span relative to boundaries of display

...

not used

Value

a ggplot instance