pcaExplorer (version 1.0.2)

pcaplot: Sample PCA plot for transformed data

Description

Plots the results of PCA on a 2-dimensional space

Usage

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

Arguments

x

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

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

text_labels

Logical, whether to display the labels with the sample identifiers

point_size

Integer, the size of the points for the samples

Value

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

Examples

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