Generic function for drawing a two-panel interactive MDS plot. The function invokes the following methods which depend on the class of the first argument:
glimmaMDS.DGEList for edgeR analysis
glimmaMDS.DESeqDataSet for DESeq2 analysis
glimmaMDS.default for all other object types
the matrix containing the gene expressions.
the additional arguments affecting the plot produced. See specific methods for detailed arguments.
The left plot shows two MDS dimensions, with sample annotations displayed on hover.
The right panel contains a bar plot of the eigenvalues of each dimension.
The controls beneath the plots can be used to change the dimensions being displayed, and the scale, colour and shape of points.
The interactive MDS plot allows users to adjust sample points by scale, colour and shape for multiple vectors associated with
sample information. This is carried out most effectively when
x$samples includes an abundance of sample information, or
when a data frame object is supplied to
groups. If a simple character or factor vector is given to
(with the default of
continous.colour=FALSE), then sample points will have no scaling options, but can only be adjusted
in colour and shape by
labels. Instead, if
groups is a numeric vector (e.g. library size or
expression level of a specific gene), then the plot can be scaled and coloured by the numeric values with
htmlwidget object or
html argument is specified.
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dge <- readRDS(system.file("RNAseq123/dge.rds", package = "Glimma")) glimmaMDS(dge) # using DESeqDataSet dds <- DESeq2::DESeqDataSetFromMatrix( countData = dge$counts, colData = dge$samples, rowData = dge$genes, design = ~group ) glimmaMDS(dds) # using matrix object expr <- edgeR::cpm(dge, log = TRUE) glimmaMDS(expr)
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