Plot RLE for a given assay within a SummarizedExperiment

plotAssayRle(x, ...)

# S4 method for class 'SummarizedExperiment'
plotAssayRle(
  x,
  assay = "counts",
  colour,
  fill,
  rle_group,
  by_x,
  n_max = Inf,
  trans = NULL,
  ...
)

Arguments

x: A SummarizedExperiment object
...: Passed to geom_boxplot
assay: The assay to plot
colour: Column from colData(x) to outline the boxplots
fill: Column from colData(x) to fill the boxplots
rle_group: Column from colData(x) to calculate RLE within groups Commonly an alternative sample label.
by_x: Boxplots will be drawn by this grouping variable from colData(x). If not specified, the default values will be colnames(x)
n_max: Maximum number of points to plot
trans: character(1). Numerical transformation to apply to the data prior to RLE calculation

Value

A ggplot2 object

Details

Uses ggplot2 to create an RLE plot for the selected assay. Any numerical transformation prior to performing the RLE can be specified using the trans argument

Examples

data("se")
se$treatment <- c("E2", "E2", "E2", "E2DHT", "E2DHT", "E2DHT")
se$sample <- colnames(se)
## A conventional RLE Plot using all samples
plotAssayRle(se, trans = "log1p", fill = "treatment")

## Calculate RLE within groups
plotAssayRle(se, trans = "log1p", fill = "treatment", rle_group = "treatment")

# Or show groups combined
plotAssayRle(se, trans = "log1p", fill = "treatment", by_x = "treatment")