plotQc: Quality control

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Quality control

Description

Quality control

Usage

plotQc(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotQc(
  object,
  assay = 1L,
  interestingGroups = NULL,
  geom = c("histogram", "ecdf", "violin", "ridgeline", "boxplot"),
  legend = getOption(x = "acid.legend", default = TRUE),
  labels = list(title = "Quality control", subtitle = NULL)
)

## S4 method for signature 'SummarizedExperiment'
plotQc(
  object,
  assay = 1L,
  interestingGroups = NULL,
  legend = getOption(x = "acid.legend", default = TRUE),
  labels = list(title = "Quality control", subtitle = NULL)
)

Arguments

object	Object.
assay	vector(1). Assay name or index position.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
geom	character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.
legend	logical(1). Include plot legend.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-08-11.

Examples

data(
    RangedSummarizedExperiment,
    SingleCellExperiment_splatter,
    package = "AcidTest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotQc(object)

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotQc(object)

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.