plotCountsPerFeature: Plot counts per feature

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Plot counts per feature

Description

Generally, we expect similar count spreads for all genes between samples unless the library sizes or total RNA expression are different.

Usage

plotCountsPerFeature(object, ...)

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

## S4 method for signature 'SummarizedExperiment'
plotCountsPerFeature(
  object,
  assay = 1L,
  interestingGroups = NULL,
  geom = c("boxplot", "density", "jitter"),
  trans = c("identity", "log2", "log10"),
  labels = list(title = "Counts per feature", subtitle = NULL, sampleAxis = NULL,
    countAxis = "counts"),
  flip = getOption(x = "acid.flip", default = TRUE),
  minMethod = c("absolute", "perRow")
)

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.
geom	character(1). Type of ggplot2 geometric object to use.
trans	character(1). Apply a log transformation (e.g. log2(x + 1L)) to the count matrix prior to melting, if desired. Use "identity" to return unmodified (default).
labels	list. ggplot2 labels. See ggplot2::labs() for details.
flip	logical(1). Flip x and y axes. Recommended for plots containing many samples.
minMethod	character(1). Only applies when min argument is numeric. Uses match.arg(). absolute: Applies hard cutoff to counts column after the melt operation. This applies to all counts, not per feature. perRow: Applies cutoff per row (i.e. gene). Internally, rowSums() values are checked against this cutoff threshold prior to the melt operation.

Value

ggplot.

Functions

• plotCountsPerFeature(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
plotCountsPerFeature(object, geom = "boxplot")
plotCountsPerFeature(object, geom = "density")

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

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