plot.reduced.dim: Plot of reduced dimensions and labels

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

Plot of reduced dimensions and labels

Description

Plot of reduced dimensions and labels

Usage

## S3 method for class 'reduced.dim'
plot(
  object,
  reduction,
  assay,
  clust.method,
  column,
  pt.size = 0.5,
  add.label = TRUE,
  label.size = NULL,
  cells = NULL,
  order = NULL,
  colours = c("Red", "Yellow", "Blue")
)

Arguments

object	An IBRAP S4 class object
reduction	Character. Which reduction to use to display points
assay	Character. Which assay within the object to access
clust.method	Character. Which clustering method to access, supply the name of any dataframe contained in the cluster_assignments sections. If you wish to access metadata, just specify 'metadata'
column	Character. Which column to access within the supplied clust.column
pt.size	Numeric. What should the point size be
cells	Numeric. Which cells should be subset for plotting, Default = NULL
colours	Vector. The first value will represent the lower value, the second the middle and the third the highest

Value

A plot of reduced dimensions annotated with assignments

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