plot_pca: Highchart version of plotPCA in DESeq2

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Highchart version of plotPCA in DESeq2

Description

Highchart version of sample PCA plot

Usage

plot_pca(
  object,
  intgroup = "trt",
  tooltip,
  label,
  ntop = 500,
  relevel,
  pc = c(1, 2),
  scale = FALSE,
  ggplot = FALSE,
  ...
)

Arguments

object	a matrix, ExpressionSet or DESeqTransform object
intgroup	a character vector of names from colData(object) or pData(object) for ExpressionSets for grouping, default 'trt'
tooltip	a character vector of names in colData(object) for tooltip display, default is id column
label	a name in colData(object) for ggplot labels
ntop	number of top variable genes to use for principal components
relevel	reorder intgroup levels, default is alphabetical
pc	a vector of components to plot, default 1st and 2nd
scale	option to scale variables in prcomp, default FALSE
ggplot	plot ggplot version, default FALSE
...	additional options passed to hc_chart

Value

A highchart

Author(s)

Chris Stubben

Examples

plot_pca(pasilla$rlog, "condition", tooltip=c("file", "type"))
plot_pca(pasilla$rlog, "condition", label="file", ggplot=TRUE)

HuntsmanCancerInstitute/hciR documentation built on Dec. 10, 2024, 12:22 p.m.