plotAssayRle-methods: Plot RLE for a given assay within a SummarizedExperiment

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

Plot RLE for a given assay within a SummarizedExperiment

Description

Plot RLE for a given assay within a SummarizedExperiment

Usage

plotAssayRle(x, ...)

## S4 method for signature '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

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

Value

A ggplot2 object

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")

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.