Sample PCA plot for transformed data

Plots the results of PCA on a 3-dimensional space, interactively

pcaplot3d(
  x,
  intgroup = "condition",
  ntop = 500,
  returnData = FALSE,
  title = NULL,
  pcX = 1,
  pcY = 2,
  pcZ = 3,
  text_labels = TRUE,
  point_size = 3
)

Arguments

x

A DESeq2::DESeqTransform() object, with data in assay(x), produced for example by either DESeq2::rlog() or DESeq2::varianceStabilizingTransformation()

intgroup

Interesting groups: a character vector of names in colData(x) to use for grouping

ntop

Number of top genes to use for principal components, selected by highest row variance

returnData

logical, if TRUE returns a data.frame for further use, containing the selected principal components and intgroup covariates for custom plotting

title

The plot title

pcX

The principal component to display on the x axis

pcY

The principal component to display on the y axis

pcZ

The principal component to display on the z axis

text_labels

Logical, whether to display the labels with the sample identifiers

point_size

Integer, the size of the points for the samples

Value

A html-based visualization of the 3d PCA plot

Examples

dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- DESeq2::rlogTransformation(dds)
pcaplot3d(rlt, ntop = 200)