plotAssayDensities-methods: Plot Densities for any assay within a SummarizedExperiment

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Plot Densities for any assay within a SummarizedExperiment

Description

Plot Densities for any assay within a SummarizedExperiment

Usage

plotAssayDensities(x, ...)

## S4 method for signature '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

Details

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

Value

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

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")

steveped/extraChIPs documentation built on June 1, 2025, 7:07 p.m.