Plot PCA matrix via GGally::ggpairs — plot_PCA

Only does "scores" PCA plots.

Usage

plot_PCA_matrix(
  df_pca,
  PCs = c(1:3),
  anno = NULL,
  annoname = "Sample",
  annotype = "Type",
  colors = NULL,
  title = NULL,
  savename = NULL,
  width = 8,
  height = 8
)

Arguments

df_pca: string/prcomp obj; (path to) PCA output with sample names in first column
PCs: num vector; list of numeric PCs to plot (ex. c(1:3) for first 3 PCs)
anno: string/df; Annotation info for DF
annoname: string; Colname in anno matching point name
annotype: string; Colname in anno with info to color by
colors: char vector; For discrete annotype, length should be number of unique annotypes.
title: string; Plot title
savename: string; File path to save plot under
width: numeric; Saved plot width
height: numeric; Saved plot height

Value

ggmatrix object with PCA scatter plot matrix

Examples

data(iris)
iris$Sample = rownames(iris)
plot_PCA_matrix(
  df_pca = Rubrary::run_PCA(t(iris[,c(1:4)]), screeplot = FALSE),
  PCs = c(1:3),
  anno = iris[,c("Sample", "Species")],
  annoname = "Sample",
  annotype = "Species",
  title = "Iris PCA"
)