plotDR: Compute and plot the results of any dimension reduction...

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

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

Description

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

Usage

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

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

## S4 method for signature '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)
plotDR(spe, dimred = "PCA")

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