plotPCA3D: Plot DESeq2's PCA plotting with Plotly 3D scatterplot

In twbattaglia/btools: A suite of R function for all types of microbial diversity analyses

Description

The function will generate a plot_ly 3D scatter plot image for a 3D exploration of the PCA.

Usage

plotPCA3D(object, intgroup = "condition", ntop = 500,
  returnData = FALSE)

Arguments

object	a DESeqTransform object, with data in assay(x), produced for example by either rlog or 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	should the function only return the data.frame of PC1, PC2 and PC3 with intgroup covariates for custom plotting (default is FALSE)

Value

An object created by plot_ly, which can be assigned and further customized.

twbattaglia/btools documentation built on May 3, 2019, 1:51 p.m.