plotMDS: Compute and plot the results of a MDS analysis on gene...

In bhuvad/restools: Research tools for data science projects

Compute and plot the results of a MDS analysis on gene expression data

Description

Compute and plot the results of a MDS analysis on gene expression data

Usage

plotMDS(edata, dims = c(1, 2), precomputed = NULL, rl = 1, ...)

## S4 method for signature 'DGEList'
plotMDS(edata, dims = c(1, 2), precomputed = NULL, rl = 1, ...)

## S4 method for signature 'ExpressionSet'
plotMDS(edata, dims = c(1, 2), precomputed = NULL, rl = 1, ...)

## S4 method for signature 'SummarizedExperiment'
plotMDS(edata, dims = c(1, 2), precomputed = NULL, rl = 1, ...)

Arguments

edata	a DGEList, SummarizedExperiment or ExpressionSet object containing gene expression data.
dims	a numeric, containing 2 values specifying the dimensions to plot.
precomputed	a dimensional reduction results from either 'limma::plotMDS'.
rl	a numeric, specifying the relative scale factor to apply to text on the plot.
...	aesthetic mappings to pass to 'ggplot2::aes_string()'.

Value

a ggplot2 object

Examples

se = emtdata::cursons2018_se()
dge = emtdata::asDGEList(se)
plotMDS(dge, colour = Subline)

bhuvad/restools documentation built on June 16, 2024, 12:44 a.m.