% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/pcaplot.R
 \name{pcaplot3d}
 \alias{pcaplot3d}
 \title{Sample PCA plot for transformed data}
 \usage{

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

 }
 \arguments{

 \item{x}{A \code{\link[DESeq2:DESeqTransform]{DESeq2::DESeqTransform()}} object, with data in \code{assay(x)},
 produced for example by either \code{\link[DESeq2:rlog]{DESeq2::rlog()}} or
 \code{\link[DESeq2:varianceStabilizingTransformation]{DESeq2::varianceStabilizingTransformation()}}}

 \item{intgroup}{Interesting groups: a character vector of
 names in \code{colData(x)} to use for grouping}
 

 \item{ntop}{Number of top genes to use for principal components,
 selected by highest row variance}
 
 \item{returnData}{logical, if TRUE returns a data.frame for further use, containing the
 selected principal components and intgroup covariates for custom plotting}
 
 \item{title}{The plot title}
 
 \item{pcX}{The principal component to display on the x axis}
 
 \item{pcY}{The principal component to display on the y axis}
 
 \item{pcZ}{The principal component to display on the z axis}
 
 \item{text_labels}{Logical, whether to display the labels with the sample identifiers}
 
 \item{point_size}{Integer, the size of the points for the samples}

 }
 \value{
 A html-based visualization of the 3d PCA plot

 }
 \description{
 Plots the results of PCA on a 3-dimensional space, interactively
 }

 \examples{

 dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)

 rlt <- DESeq2::rlogTransformation(dds)

 pcaplot3d(rlt, ntop = 200)

 }