Plot counts per biotype

Plot counts per biotype

Usage

plotCountsPerBiotype(object, ...)

plotCountsPerBroadClass(object, ...)

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

# S4 method for 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

Michael Steinbaugh, Rory Kirchner

Examples

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

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
plotCountsPerBiotype(object)
#> ℹ 499 / 500 features passed `perRow` >= "1" cutoff.


## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotCountsPerBiotype(object)
#> ℹ 100 / 100 features passed `perRow` >= "1" cutoff.