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

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

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(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

## S4 method for signature 'DGEList'
plotMDS(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

## S4 method for signature 'ExpressionSet'
plotMDS(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

## S4 method for signature 'SummarizedExperiment'
plotMDS(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

## S4 method for signature 'SingleCellExperiment'
plotMDS(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

## S4 method for signature 'SpatialExperiment'
plotMDS(
  object,
  dims = c(1, 2),
  precomputed = NULL,
  textScale = 1,
  assay = 1,
  ...
)

Arguments

object	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.
textScale	a numeric, specifying the relative scale factor to apply to text on the plot.
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment and its derivative classes).
...	aesthetic mappings to pass to ggplot2::aes_string().

Value

a ggplot2 object

Examples

data("dkd_spe_subset")
standR::plotMDS(dkd_spe_subset)

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.