plotCountsPerBiotype: Plot counts per biotype

In acidgenomics/r-acidplots: Acid Genomics Plot Functions and Themes

Plot counts per biotype

Description

Plot counts per biotype

Usage

plotCountsPerBiotype(object, ...)

plotCountsPerBroadClass(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotCountsPerBiotype(
  object,
  assay = 1L,
  biotypeCol = "geneBiotype",
  n = 9L,
  interestingGroups = NULL,
  geom = c("violin", "boxplot"),
  trans = c("identity", "log2", "log10"),
  labels = list(title = "Counts per biotype", subtitle = NULL, sampleAxis = NULL,
    countAxis = "counts")
)

## S4 method for signature 'SummarizedExperiment'
plotCountsPerBiotype(
  object,
  assay = 1L,
  biotypeCol = "geneBiotype",
  n = 9L,
  interestingGroups = NULL,
  geom = c("violin", "boxplot"),
  trans = c("identity", "log2", "log10"),
  labels = list(title = "Counts per biotype", subtitle = NULL, sampleAxis = NULL,
    countAxis = "counts")
)

## S4 method for signature 'SingleCellExperiment'
plotCountsPerBroadClass(
  object,
  ...,
  labels = list(title = "Counts per broad class biotype", subtitle = NULL, sampleAxis =
    NULL, countAxis = "counts")
)

## S4 method for signature 'SummarizedExperiment'
plotCountsPerBroadClass(
  object,
  ...,
  labels = list(title = "Counts per broad class biotype", subtitle = NULL, sampleAxis =
    NULL, countAxis = "counts")
)

Arguments

object	Object.
assay	vector(1). Assay name or index position.
biotypeCol	character(1). Biotype column name defined in colData().
n	integer(1). Number to include.
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.
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-12-04.

Author(s)

Michael Steinbaugh, Rory Kirchner

Examples

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

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

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

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