Plot Densities for any assay within a SummarizedExperiment

plotAssayDensities(x, ...)

# S4 method for class 'SummarizedExperiment'
plotAssayDensities(
  x,
  assay = "counts",
  group = NULL,
  colour = NULL,
  fill = NULL,
  linetype = NULL,
  linewidth = NULL,
  alpha = NULL,
  trans = NULL,
  n_max = Inf,
  ...
)

Arguments

x: A SummarizedExperiment object
...: Passed to geom_density
assay: An assay within x
group: Used by geom_line. Defaults to the column names but treatment groups can also be specified to summarise within groups
colour, fill, alpha: Optional column in colData to set the respective aesthetics. Can also be any valid colour specification as a fixed value or a fixed alpha value
linetype, linewidth: Any optional column in colData used to determine linetype or linewidth. Can also be fixed values
trans: character(1). Any transformative function to be applied to the data before calculating the density, e.g. trans = "log2"
n_max: Maximum number of points to use when calculating densities

Value

A ggplot2 object. Scales and labels can be added using conventional ggplot2 syntax.

Details

Uses ggplot2 to create a density plot for all samples within the selected assay

Examples

data("se")
se$treatment <- c("E2", "E2", "E2", "E2DHT", "E2DHT", "E2DHT")
## Plot individual samples
plotAssayDensities(se, colour = "treatment")

## Plot combined within treatment groups
plotAssayDensities(se, colour = "treatment", group = "treatment")

## Use a data transformation
plotAssayDensities(se, trans = "log1p", colour = "treat")