plotFeatureSaturation: Plot feature (gene) detection saturation

In hbc/bcbioRnaseq: Bcbio RNA-Seq

Plot feature (gene) detection saturation

Description

We should observe a linear trend in the number of genes detected with the number of mapped reads, which indicates that the sample input was not overloaded.

Usage

plotFeatureSaturation(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotFeatureSaturation(
  object,
  interestingGroups = NULL,
  minCounts = 1L,
  perMillion = TRUE,
  trendline = FALSE,
  label = getOption(x = "acid.label", default = FALSE),
  labels = list(title = "Gene saturation", subtitle = NULL, x = "mapped reads", y =
    "gene count")
)

Arguments

object	Object.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
minCounts	integer(1). Minimum number of counts per feature (i.e. gene).
perMillion	logical(1). Display as counts per million.
trendline	logical(1). Include trendline on plot.
label	logical(1). Superimpose sample text labels on the plot.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-10-05.

Author(s)

Michael Steinbaugh, Rory Kirchner, Victor Barrera

Examples

data(bcb)

## bcbioRNASeq ====
plotFeatureSaturation(bcb, label = FALSE)
plotFeatureSaturation(bcb, label = TRUE)

hbc/bcbioRnaseq documentation built on Sept. 15, 2024, 9:10 a.m.