plotQc: Quality control

plotQcR Documentation

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/r-acidplots documentation built on March 30, 2024, 10:16 p.m.