plot.features: Plot of reduced dimensions and features

In connorhknight/IBRAP: Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP)

Plot of reduced dimensions and features

Description

Plot of reduced dimensions and features

Usage

## S3 method for class 'features'
plot(
  object,
  assay,
  slot,
  reduction,
  features,
  order = TRUE,
  percentile = c(0, 1),
  pt_size = 0.5,
  cells = NULL,
  colours = c("#C0C0C0", "#4169E1")
)

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
colours	Vector. The first value will represent the lower values and the second the highest
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

connorhknight/IBRAP documentation built on March 9, 2023, 7:01 p.m.