Compute and plot the results of any dimension reduction methods on gene expression data — plotDR • standR

Compute and plot the results of any dimension reduction methods on gene expression data

plotDR(object, dims = c(1, 2), ...)

# S4 method for SingleCellExperiment
plotDR(object, dims, dimred = "PCA", textScale = 1, ...)

# S4 method for SpatialExperiment
plotDR(object, dims, dimred = "PCA", textScale = 1, ...)

Arguments

object: a DGEList, SummarizedExperiment or ExpressionSet object containing gene expression data.
dims: a numeric, containing 2 values specifying the dimensions to plot.
...: aesthetic mappings to pass to ggplot2::aes_string().
dimred: a string or integer scalar indicating the reduced dimension result in reducedDims(object) to plot.
textScale: a numeric, specifying the relative scale factor to apply to text on the plot.

Value

a ggplot2 object

Examples

library(scater)
data("dkd_spe_subset")
spe <- scater::runPCA(dkd_spe_subset)
#> Warning: You're computing too large a percentage of total singular values, use a standard svd instead.
plotDR(spe, dimred = "PCA")