plotPairPCA: Plot pair-wise PCA plots for multiple dimensions

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

Plot pair-wise PCA plots for multiple dimensions

Description

Plot pair-wise PCA plots for multiple dimensions

Usage

plotPairPCA(
  spe_object,
  n_dimension = 3,
  precomputed = NULL,
  assay = 2,
  title = NA,
  title.size = 14,
  rmduplabs = FALSE,
  flipcoord = FALSE,
  legend.pos = "top",
  ...
)

Arguments

spe_object	A SpatialExperiment object.
n_dimension	The top n dimensions to be plotted
precomputed	a dimensional reduction results from stats::prcomp. result in reducedDims(object) to plot. Default is NULL, we will compute for you.
assay	a numeric or character, specifying the assay to use (for SummarizedExperiment and its derivative classes).
title	Character vector, title to put at the top.
title.size	Numeric vector, size of the title.
rmduplabs	Remove duplicated labels from the plot. FALSE by default.
flipcoord	Flip the xy coordinates. FALSE by default.
legend.pos	Position of the legend. top by default.
...	aesthetic mappings to pass to ggplot2::aes().

Value

A ggplot object.

Examples

data("dkd_spe_subset")
plotPairPCA(dkd_spe_subset)

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