plotPCAbiplot: Plot PCA bi plot

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

Plot PCA bi plot

Description

Plot PCA bi plot

Usage

plotPCAbiplot(
  spe_object,
  n_loadings = 10,
  dims = c(1, 2),
  precomputed = NULL,
  assay = 1,
  arrow_x = 0,
  arrow_y = 0,
  ...
)

Arguments

spe_object	A SpatialExperiment object.
n_loadings	Plot the top n gene loadings
dims	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).
arrow_x	a numeric, indicating the x coordinate of the base of the arrow.
arrow_y	a numeric, indicating the y coordinate of the base of the arrow.
...	aesthetic mappings to pass to ggplot2::aes().

Value

A ggplot object.

Examples

data("dkd_spe_subset")
plotPCAbiplot(dkd_spe_subset)

DavisLaboratory/standR documentation built on March 28, 2024, 4:23 a.m.