Quality control

Usage

plotQc(object, ...)

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

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

Arguments

object: 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.
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.
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)
#> Ignoring unknown labels:
#> • colour : "sampleName"
#> Ignoring unknown labels:
#> • colour : "sampleName"
#> Ignoring unknown labels:
#> • colour : "sampleName"