Plot of reduced dimensions and features

Plot of reduced dimensions and features

# S3 method for features
plot(
  object,
  assay,
  slot,
  reduction,
  features,
  order = TRUE,
  percentile = c(0, 1),
  pt_size = 0.5,
  cells = NULL
)

Arguments

object

An IBRAP S4 class object

assay

Character. Which assay within the object to access

slot

Character. Which expression matrix would you like to access. Default = 'normalised'

reduction

Character. Which reduction should be used for the plot

features

Character Which features should be plotted

order

Boolean. Should datapoints be plotted in order of expression intensity. Default = TRUE

pt_size

Numeric. what size should the inidividual plot sizes be

cells

Numeric. Which cells should be subset for plotting, Default = NULL

percentile.

Numerical. What percentile of datapoint expression should be plotted. Default = c(0.1,0.9)

Value

A plot of reduced dimensions annotated with assignments