plotFeaturesDetected: Plot features detected

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Plot features detected

Description

Visualize the number of features (i.e. genes) detected.

Usage

plotFeaturesDetected

## S4 method for signature 'SingleCellExperiment'
plotFeaturesDetected(object, ...)

## S4 method for signature 'SummarizedExperiment'
plotFeaturesDetected(
  object,
  assay = 1L,
  interestingGroups = NULL,
  limit = 0L,
  minCounts = 1L,
  labels = list(title = "Features detected", subtitle = NULL, x = NULL, y = "features"),
  flip = getOption(x = "acid.flip", default = TRUE)
)

Arguments

object	Object.
...	Additional arguments.
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.
limit	numeric(1). Threshold limit.
minCounts	integer(1). Minimum number of counts per feature (i.e. gene).
labels	list. ggplot2 labels. See ggplot2::labs() for details.
flip	logical(1). Flip x and y axes. Recommended for plots containing many samples.

Value

ggplot.

Functions

• plotFeaturesDetected(SingleCellExperiment): Applies aggregateCellsToSamples() calculation to summarize at sample level prior to plotting.
  Passes ... to SummarizedExperiment method.

Note

Updated 2023-08-11.

Examples

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

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

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

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