Plot PCA with arrows — plot_pca

Plot PCA with arrows indicating trajectory over time, for a single group.

Usage

plot_pca_arrows(
  se_obj,
  circle = TRUE,
  arrow = TRUE,
  pc1 = 1,
  pc2 = 2,
  fontsize = 8,
  assay = 1
)

se_obj: A SummarizedExperiment object (single group).
circle: Logical, whether to draw ellipses around samples of each time point (default: TRUE).
arrow: Logical, whether to draw arrows indicating the trajectory over time (default: TRUE).
pc1: Principal component for the x-axis (default: 1).
pc2: Principal component for the y-axis (default: 2).
fontsize: Base font size (default: 8).
assay: Assay index to use, where 1 is the original data and 2 is normalised to time 0 (if available) (default: 1).

A PCA plot coloured by Time, with optional ellipses and trajectory arrows.

data(example_obj)
plot_pca_arrows(example_obj[, example_obj$Group == "IFNbeta"])
#> Warning: Using size for a discrete variable is not advised.