plotAssayPCA-methods: Plot PCA For any assay within a SummarizedExperiment

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

Plot PCA For any assay within a SummarizedExperiment

Description

Plot PCA for any assay within a SummarizedExperiment object

Usage

plotAssayPCA(x, ...)

## S4 method for signature 'SummarizedExperiment'
plotAssayPCA(
  x,
  assay = "counts",
  colour,
  shape,
  size,
  label,
  show_points = TRUE,
  pc_x = 1,
  pc_y = 2,
  trans = NULL,
  n_max = Inf,
  tol = sqrt(.Machine$double.eps),
  rank = NULL,
  ...
)

Arguments

x	An object containing an assay slot
...	Passed to geom_text
assay	The assay to perform PCA on
colour	The column name to be used for colours
shape, size	The column name(s) to be used for determining the shape or size of points
label	The column name to be used for labels
show_points	logical(1). Display the points. If TRUE any labels will repel. If FALSE, labels will appear at the exact points
pc_x	numeric(1) The PC to plot on the x-axis
pc_y	numeric(1) The PC to plot on the y-axis
trans	character(1). Any transformative function to be applied to the data before performing the PCA, e.g. trans = "log2"
n_max	Subsample the data to this many points before performing PCA
tol	Any rows with variance below this value will be excluded prior to passing to prcomp. All rows are scaled and centred by default
rank	Passed to prcomp

Details

Uses ggplot2 to create a PCA plot for the selected assay. Any numerical transformation prior to performing the PCA 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)
plotAssayPCA(se, trans = "log1p", colour = "treatment", label = "sample")
plotAssayPCA(
  se, trans = "log1p", colour = "treatment", label = "sample",
  size = totals / 1e3
)
plotAssayPCA(
  se, trans = "log1p", colour = "treatment", label = "sample",
  show_points = FALSE
)

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