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

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

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

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

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

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

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

# S4 method for 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)