drawPCA: Compute and plot the results of a PCA analysis on gene...

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

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

Description

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

Usage

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

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

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

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

## S4 method for signature 'SpatialExperiment'
drawPCA(
  object,
  dims = c(1, 2),
  assay = 1,
  precomputed = NULL,
  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().
precomputed	a dimensional reduction results from stats::prcomp. result in reducedDims(object) to plot.
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).

Value

a ggplot2 object

Examples

data("dkd_spe_subset")
drawPCA(dkd_spe_subset)

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