plotQC {scater}R Documentation

Produce QC diagnostic plots

Description

Produce QC diagnostic plots

Usage

plotQC(object, type = c("highest-expression", "find-pcs",
  "explanatory-variables", "exprs-freq-vs-mean"), ...)

Arguments

object

A SingleCellExperiment object.

type

String specifying the type of QC plot to compute.

...

Arguments passed to further plotting functions.

Details

This is a wrapper function to call a variety of different plotting functions. It has been deprecated in favour of calling the target functions specifically, which involves less typing anyway!

Value

A ggplot plot object.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
example_sce <- SingleCellExperiment(
  assays = list(counts = sc_example_counts), 
  colData = sc_example_cell_info)
example_sce <- normalize(example_sce)

example_sce <- calculateQCMetrics(example_sce)
plotQC(example_sce, type="high", colour_cells_by="Mutation_Status")

[Package scater version 1.10.1 Index]